Tag: SNAKEMAKE

Amplifybio, LLC Sr./Scientist, Bioinformatics in South San Francisco, CA | 892968472

Are you passionate about significantly improving the future of medicine? Do you believe that people are the most important asset of any company? If so, join AmplifyBio! AmplifyBio is a company dedicated to building an integrated environment where clients can access technologies, platforms, capabilities and safety testing for the scale…

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Bioinformatics scientist | GENOMINES

Job Description Who we are Genomines is a young biotechnology company based in Paris and Saclay, specialized in sustainable extraction of Nickel from plants. The mission of Genomines is to usher in a new era of sustainable mining by using genetically enhanced plants to extract metals from soil (agromining). Through…

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‘Resources’ object has no attribute ‘tmpdir’

Snakemake error AttributeError: ‘Resources’ object has no attribute ‘tmpdir’ 0 I have built a Snakemake pipeline which has been designed for paired-end reads. I have made a trial with single-end reads, and got this error. I am not sure it is related to the change of reads design, and to…

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MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes

Abstract Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions, and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced…

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Snakemake rule error

Snakemake rule error 0 I have the following rule in snakemake: rule low_coverage_contig_reads: input: bam=”data/processed/bam_files/bam/{sample}_{fraction}.bam.bai”, output: r1=”data/processed/clean_reads/low_cov/low_cov_{sample}_{fraction}_R1.fq.gz”, r2=”data/processed/clean_reads/low_cov/low_cov_{sample}_{fraction}_R2.fq.gz” threads: 8 params: bam=”data/processed/bam_files/bam/{sample}_{fraction}.bam” log: log1=”logs/{sample}_{fraction}_low_coverage_reads.log”, shell: “”” (samtools coverage {params.bam} | awk ‘NR > 1 && $7 < 10 {{print $1}}’ | tr ‘\\n’ ‘ ‘ | samtools view -u {params.bam}…

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How to input list into GenomicsDBImport with snakemake?

How to input list into GenomicsDBImport with snakemake? 0 Hello! I’m currently writing a pipeline with snakemake for exome data. During joint variant calling I need to use GATK’s GenomicsDBImport, although I’m unsure how to input all the samples at once. Here’s the simplified version of the rule I’m using:…

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Bioinformatics Machine Learning Engineer – Biomedial Diagnostics – German Language Skills job with Umbilical Life

I am currently working with several clients across EU looking for Biomedical Data Scientists / ML Engineers for applications in R&D. My client based in Munich are searching for ML engineers for applications in Bioinformatics & Diagnostics.  German Language skills are essential for this client (B2 and above). Responsibilities  …

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Vacature Postdoc position in Bioinformatics

In this TKI-PPP funded project, our objective is to construct a comprehensive landscape of the tumor microenvironment in cervical cancer patients and investigate its potential clinical applications using cutting-edge bioinformatic and molecular profili… Cervical cancer ranks fourth leading causes of cancer death in women globally, with approximately 800-900 diagnosis annually…

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Telethon Kids Institute hiring Bioinformatics Engineer in Perth, Western Australia, Australia

The Opportunity We are seeking a highly skilled and motivated Bioinformatics Engineer to join our Indigenous Genomics team, here at the Telethon Kids Institute. The Indigenous Genomics team operates out of Perth, Adelaide and Melbourne, and comprises a diverse, multi-disciplinary, Indigenous-led group of professionals and researchers, with expertise across genomics,…

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DS Group hiring Bioinformatician in London, England, United Kingdom

Bioinformatician – Deep Learning, Python, PyTorch, GWAS, RNA At the company, a leading agbiotech start-up, safeguarding the future of food is at the heart of what drives and inspires every member of the team. With a mission to accelerate the development of more productive, sustainable, nutritious, and climate-resilient food sources,…

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Arcadia Science hiring Scientist, Protein Bioinformatics in Berkeley, CA, US

About Arcadia Science Arcadia Science is pushing the boundaries of open science and innovating at every step in the research, development, and commercialization process. Job Description A Bit About Us:   We are Arcadia Science. Arcadia is a science company founded and led by scientists. Our mission is to transform…

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Head of the Medical Bioinformatics platform (m/f/d) – Kiel

Das Universitätsklinikum Schleswig-Holstein (UKSH) verbindet internationale Spitzenforschung mit interdisziplinärer Krankenversorgung. Wir sind einziger Maximalversorger und größter Arbeitgeber des Landes. Unsere mehr als 14.500 Mitarbeiter*innen stellen eine höchst individuelle Versorgung sicher – unverzichtbar für die Menschen in Schleswig-Holstein.The Institute of Clinical Molecular Biology (IKMB)The Medical Faculty together with the Institute of…

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resources – Snakemake, slurm and memory

I am struggling to understand how snakemake submits jobs to slurm. When I have a basic slurm sbatch script I usually add a line, such as #SBATCH –mem=5Gto determine that slurm may use 5 gigabytes (and no more) of memory. Now, I am using snakemake together with slurm with snakemake…

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Is there a good software to generate test genomics data?

Is there a good software to generate test genomics data? 0 For example if I input a reference genome FASTA can I get simulated FASTQ files for ONT sequencing or PacBio sequencing runs that could have produced that data? I’m trying to migrate over from Snakemake to Nextflow but from…

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Sr Scientist I, Bioinformatics Engineer job with AbbVie

The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…

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Advisor/Sr. Advisor – Bioinformatics – Relocation Assistance job with Lilly

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease,…

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Head of Bioinformatics Job in Greater London, Career, Permanent Jobs in Bactobio

We are looking for an exceptional microbial bioinformatician to join our leadership team at Bactobio as Head of Bioinformatics. Company Bactobio is a London-based biotechnology company founded in 2020. We use breakthrough technologies in synthetic biology, next-generation sequencing, and machine learning to cultivate the 99% previously unculturable microbes. These…

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Lilly Advisor/Sr. Advisor – Bioinformatics in New York, NY | 883515845

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease,…

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Samtools index not working in Snakemake

I am setting up a Snakemake pipeline for sequencing reads alignment and variants calling. But the samtools index rule is not activated, and the subsequent haplotype caller rule fail. I think it is because the samtools index rule is not perceived as necessary to execute the output of rule all…

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ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications | BMC Bioinformatics

Pipeline architecture and configuration file Genomic data processing poses a challenge for genetic research studies because it involves multiple program dependency installations, vast numbers of samples with raw data from various next-generation sequencing (NGS) platforms, and inconsistent genetic variant ID and/or positions among datasets. The Iliad suite of genomic data…

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Post Doctoral Fellow job with University of Missouri – Columbia

Job Description Bond Lifesciences Center would like to hire up to two Post Doctoral Fellows. Duties would include: (1) Analyze diverse types of biological data, including next generation sequencing (NGS) such as RNA-seq, single cell RNA-seq, and others, multiomics data integration and microbiome data. Prepare and publish manuscripts and reports….

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Data Engineer II, Bioinformatics at Flagship Pioneering, Inc. – Cambridge, MA USA

Company Summary: Arana Biosciences is one of the latest companies founded through Flagship Pioneering’s venture creation engine, where companies such as Moderna Inc. and Indigo Ag were conceived and created. Since Flagship’s founding in 2000, the firm has originated and fostered the development of nearly 100 scientific ventures resulting in…

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Snakemake issue with wrappers

I have issues when running a wrapper of BWA mem with Snakemake. The error message “No module named ‘snakemake_wrapper_utils’” appear (see below). However, when checking if the package is installed in Python, I found the following: import snakemake_wrapper_utils print(snakemake_wrapper_utils.__version__) 0.1.0 Did anyone have this problem? Would you know why there…

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An extremely fast Non-Overlapping Exon Length calculator written in Rust

Hi all! Introducing the Non-Overlapping Exon Length calculator (NOEL), an extremely fast GTF/GFF per gene exon length extractor written in Rust. See the code and latest updates here: github/alejandrogzi/noel In case you do not want to read the whole text: NOEL outperforms all open-sourced scripts/tools for this task. It can…

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Arcadia Science hiring Scientist, Protein Bioinformatics in Berkeley, California, United States

A Bit About UsWe are Arcadia Science. Arcadia is a science company founded and led by scientists. Our mission is to transform evolutionary innovations into real-world solutions by openly developing more efficient, replicable, and sustainable ways to leverage the biology of diverse organisms. The Opportunity We are looking for an…

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Bioinformatics Machine Learning Engineer – Biomedial Diagnostics job with Umbilical Life

I am currently working with several clients across EU looking for Biomedical Data Scientists / ML Engineers for applications in R&D. My client based in Munich are searching for ML engineers for applications in Bioinformatics & Diagnostics.  Responsibilities  ML and AI analysis of biological data  Prototyping, developing and…

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python – Error in snakemake when running conda envs in container

I am facing an issue when running snakemake with a container and conda. Let me explain better. I am developing a workflow (locally) in snakemake, where some rules use a conda env (defined in /envs/env.yaml) and other rules use wrappers (so they also are based on conda envs). An example…

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Research Officer | Jobs/Training Opportunities

Reports To:  Study Principal Investigator Directly Supervises: None Indirectly Supervises: None Budget and Resource Responsibility: None. Key Responsibilities: To develop bioinformatics tools suitable for general-purpose computing environments that support federated analysis of genomic data Develop and curate reproducible bioinformatics pipelines for analysis of genomic data using SnakeMake and Nextflow.  Develop data analysis…

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NatureMetrics hiring Bioinformatics Engineer in Guildford, England, United Kingdom

Bioinformatics Engineer – Introduction If you have a PhD in bioinformatics or computational biology and/or experience in developing NGS pipelines in a commercial or high-throughput genomics environment. We are a science-based SME with a bright future. We have an exciting scale up plan backed by ambitious and supportive investors and…

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Booz Allen Hamilton hiring Bioinformatics Specialist in Atlanta, GA

Job Number: R0182249Bioinformatics Specialist The Challenge: Are you excited at the prospect of unlocking the secrets held by a data set? Are you fascinated by the possibilities presented by the IoT, machine learning, and artificial intelligence advances? In an increasingly connected world, massive amounts of structured and unstructured data open…

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NLB Services hiring Bioinformatics Analyst in Mississauga, Ontario, Canada

Greetings for the day, Please find the details of position below: Job Title: Image Analyst Location: Mississauga, ON – (Hybrid -3 Days onsite/ Week) Duration: 12+ Months Job Description Principal Duties and Responsibilities: · Under the supervision of project manager, investigate and apply the best-in-class algorithms to process raw microscopy…

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Wildcards in Snakemake

I wish to input the names of my samples in a table with the corresponding files of reads forward and reverse to use them in a Snakemake workflow: sample fq1 fq2 1 ../reads/110627_0240_AC0254ABXX_2_SA-PE-001.1.fq.gz ../reads/110627_0240_AC0254ABXX_2_SA-PE-001.2.fq.gz 2 ../reads/110627_0240_AC0254ABXX_2_SA-PE-002.1.fq.gz ../reads/110627_0240_AC0254ABXX_2_SA-PE-002.2.fq.gz 22 ../reads/110802_0249_AD0CM0ABXX_3_SA-PE-022.1.fq.gz ../reads/110802_0249_AD0CM0ABXX_3_SA-PE-022.2.fq.gz Unfortunately, the management of the wildcards is more complex and…

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Antiviral type III CRISPR signalling via conjugation of ATP and SAM

Cloning Supplementary Table 1 shows the synthetic gene, DNA and RNA oligonucleotide sequences used in this study. The synthetic genes encoding B.fragilis Cas6, CorA, NrN and C. botulinum SAM lyase purchased as g-blocks (IDT) were codon-optimized for expression in E. coli C43 (DE3) via the vector pEhisV5TEV, which encodes eight…

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BioSpace hiring Advisor/Sr. Advisor – Bioinformatics in Cambridge, MA

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our 35,000 employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of…

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python – Send email after Snakemake workflow finishes successfully on SLURM

Is there way to send an email after a Snakemake workflow finished when using the –slurm option? Something like this: onsuccess: email([email protected], title=”Snakemake job xxx finished successfully”) onerror: email([email protected], title=”Snakemake job xxx failed”) SLURM scripts have this option: #!/bin/bash #SBATCH –mail-type=END,FAIL I would not like an email after each rule…

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BioSpace hiring Scientist, Bioinformatics Engineer in South San Francisco, California, United States

The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…

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Broad Institute of MIT and Harvard hiring Principal Bioinformatics Engineer in Cambridge, Massachusetts, United States

Job DescriptionThe Cancer Data Science (CDS) team at the Broad (www.cancerdatascience.org/) is an interdisciplinary group dedicated to accelerating cancer research. We help design and analyze large-scale experiments, develop new statistical tools and machine learning methods, write papers, produce datasets used by tens of thousands of researchers around the world, and…

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ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

Abstract Background: Processing raw genomic data for downstream applications such as imputation, association studies, and modeling requires numerous third-party bioinformatics software tools. It is highly time-consuming and resource-intensive with computational demands and storage limitations that pose significant challenges that increase cost. The use of software tools independent of one another,…

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MUSC College of Health Professions hiring UNIV – Research Specialist III- Bioinformatician – Department of Neuroscience in Charleston, South Carolina, United States

Job Description SummaryThe brand-new MUSC Bioinformatics Core (BioCM) is seeking a superb bioinformatician to develop scientific tools for single cell multiomics and other next-generation sequencing methods. Under the supervision and guidance of BioCM staff and Dr. Stefano Berto, the bioinformatician will contribute to NGS analysis projects, and they will work…

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Docker image to use Rscript

Hi! I am having some issues combining docker with snakemake workflows. I have some rules that involve running an R script on the input(s) and producing some output(s). Until now, I’ve also been able to solve the environments for these R scripts with conda environments , however, I’m now at…

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Amplifybio, LLC Sr./Scientist, Bioinformatics in South San Francisco, CA | 876106342

Are you passionate about significantly improving the future of medicine? Do you believe that people are the most important asset of any company? If so, join AmplifyBio! AmplifyBio is a company dedicated to building an integrated environment where clients can access technologies, platforms, capabilities and safety testing for the scale…

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Exact Sciences hiring Senior Director, Bioinformatics in San Diego, California, United States

Position OverviewSenior Director, Bioinformatics will lead a team of Bioinformatics Scientists and Engineers in high-dimensional genomics data analysis, method development, and pipeline prototyping to ensure the accurate detection of biological signal(s) and successful and timely completion of large and complex multi-omics cancer liquid biopsy product development. The Sr Director, Bioinformatics…

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Scribe Therapeutics hiring Scientist II/Sr. Scientist, Bioinformatics in Alameda, California, United States

Scribe Therapeutics is a molecular engineering company focused on creating best-in-class in vivo therapies that permanently treat the underlying cause of disease. Founded by CRISPR inventors and leading molecular engineers Benjamin Oakes, Brett Staahl, David Savage, and Jennifer Doudna, Scribe is overcoming the limitations of current genome editing technologies by…

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Manage the wrappers in Snakemake

I am trying to make a Snakemake pipeline using a configuration file config.yaml. — samples: – Sample_1: reads/raw_reads_1 – Sample_2: reads/raw_reads_2 – Sample_3: reads/raw_reads_3 reference: – “path/to/reference.fasta” … Following the good practices given in the Snakemake wrapper repository, I have used wrappers commands as much as possible. snakemake-wrappers.readthedocs.io/en/stable/ However I…

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Senior Bioinformatics Scientist – Jobs South Africa

Location Not specified, Full Time Deadline: Not specified Position summaryAs a Senior Bioinformatics Scientist, you will provide bioinformatics support for product research and development, as well as the marketing, sales and on-market product support teams. You will collaborate and innovate with bioinformatics scientists, software engineers and  molecular biologists to build…

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Snakemake alignment script

I have been trying to write a simple alignment pipeline with Snakemake. Unfortunately, I have a hard time understanding the error messages. In the example below, the message ” ‘str’ object has no attribute ‘name’ ” is a bit cryptic. Does it means that the expression {input.r1} is incorrect? import…

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Snakemake task fails on SLURM without error – how to debug?

I try to run multiple tasks via SLURM using snakemake –slurm -j 200. Some of the SLURM jobs fail but I cannot find any error message. snakemake prints the following: … [Thu Sep 28 10:25:04 2023] Error in rule optimize_network: message: SLURM-job ‘783028’ failed, SLURM status is: ‘FAILED’ jobid: 142…

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Moderna hiring Engineer I, Bioinformatics in Cambridge, Massachusetts, United States

The RoleThe Engineer I, Bioinformatics will develop computational protein engineering and bioinformatics pipelines and implement novel algorithms internally to support the Research and Early Development efforts for cancer vaccine related programs. You will work closely with computational scientists, bioinformaticians, statisticians, engineers and laboratory scientists within Oncology and cancer therapeutics teams…

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Research Associate in Bioinformatics (m/f/d) job with TECHNISCHE UNIVERSITAT DRESDEN (TU DRESDEN)

TUD Dresden University of Technology, as a University of Excellence, is one of the leading and most dynamic research institutions in the country. Founded in 1828, today it is a globally oriented, regionally anchored top university as it focuses on the grand challenges of the 21st century. It develops innovative…

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cluster computing – Snakemake: Handling Preempted Jobs on Slurm: Issues with Job Status and Cleanup

This message follows up on the one posted two years ago (Snakemake: Job preemption can interrupt running jobs on clusters, how to make sure that the task is not considered as failed?). I no longer encounter the described bug (IncompleteFilesException), but I still haven’t managed to handle preempted jobs properly….

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University of Washington hiring Bioinformatics Specialist, Software Engineer in Seattle, Washington, United States

Req #: 227105 Department: GENOME SCIENCES Posting Date: 09/20/2023 Closing Info: Open Until Filled Salary: $6,843 to $7,917 per month Shift: First Shift Notes: As a UW employee, you will enjoy generous benefits and work/life programs. For a complete description of our benefits for this position, please visit our website,…

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Elusive syntax error in Snakefile

Elusive syntax error in Snakefile 0 Hi, I’m quite new to snakemake and was trying to write a little workflow to analyze some nanopore data. However, it keeps returning an invalid syntax error caused by this rule rule alignment: input: “{base_out}/2.TRIMMING/{sample}.trimmed_and_clean.fastq.gz” output: “{base_out}/3.ALIGNMENT/{sample}.ngmlr.bam”, “{base_out}/3.ALIGNMENT/{sample}.ngmlr.bai” resources: partition: “EPYC” runtime: 5760 mem_mb:…

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RNA-seq workflow using STAR and DESeq2

log <- file(snakemake@log[[1]], open = “wt”) sink(log) sink(log, type=”message”) library(stringr) library(“DESeq2”) parallel <- FALSE if (snakemake@threads > 1) { library(“BiocParallel”) # setup parallelization register(MulticoreParam(snakemake@threads)) parallel <- TRUE } counts_data <- read.table( snakemake@input[[“counts”]], header = TRUE, row.names = “gene”, check.names = FALSE ) counts_data <- counts_data[, order(names(counts_data))] col_data <- read.table( snakemake@config[[“samples”]],…

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Scientist, Bioinformatics Engineer – South San Francisco

The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human…

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A list of technical advantages of Snakemake over Nextflow

Blog:A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake 0 To summarize: Python is the lingua franca of bioinformatics Nextflow’s DSL is overbearing and inconsistently uses Groovy Nextflow channels / tuples lack static type checking and prevent code reuse Snakemake is easier to debug (line…

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Roche hiring Principal Scientist I Bioinformatics in Mississauga, Ontario, Canada

The PositionRoche Sequencing Solutions (RSS), a business within Roche Diagnostics, focused on developing a disruptive Next-Generation Sequencing (NGS) platform along with a portfolio of reagents, assays and informatics solutions for multiple disease areas. We are looking for a Principal Bioinformatics Scientist in the NGS Algorithms and Applications team to support…

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Senior Bioinformatics Scientist – England

Job Description Role: Senior Bioinformatics Scientist Opportunity to join a World Class clinical stage Biotech, focused within the oncology space as a Senior Bioinformatician. Responsibilities: Involved in experimental design of new datasets being generated. To develop, deploy and document software for the automation of processing, quality control and dissemination of…

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Director, Bioinformatics – Richmond | Mendeley Careers

Title: Director, Bioinformatics Manager: VP, Bioinformatics Department: ResearchLocation: Richmond / Remote Sangamo Therapeutics is a genomic medicine company building value with cutting-edge work across four distinct but complementary technology platforms – gene therapy, cell therapy, in vivo genome editing, and in vivo genome regulation. Using its deep scientific expertise and…

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python – Run command when creating Conda environment with Snakemake

I presume that downloading script produces some output. I would split your rule into two rules, one specifically for downloading and the other only for running the annotation. The downloading rule will have declared only the output directive, which would be the input for the second rule. rule download_genome: output:…

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Bioinformatics Intern – HaystackAnalytics | Mumbai, Maharashtra

HaystackAnalytics is a company working in deep technology of genomics, computing, and data science for creating the first of its kind clinical reporting engine in healthcare. We are a new but well- funded company with a tremendous amount of pedigree in the team (IIT Founders, IIT & IIM core team)….

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GreenLight Biosciences hiring Bioinformatics Scientist in Triangle, North Carolina, United States

About GreenlightAt GreenLight we are working to solve two of the world’s greatest problems: global food insecurity and equal access to vaccines and the associated health benefits. Unlike most corporations who can be required to put profits ahead of other principles, GreenLight is one of the first Public Benefit Corporations…

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Postdoctoral Fellow, Virology job with UNIVERSITY OF NEW SOUTH WALES

Employment Type: Full – time (35 hours a week) Duration: 1-Year Fixed Term contract (with possible 2-year extension) Remuneration: Up to $106,337 p.a. (+17% super and leave loading) Location: Prince of Wales Hospital, Randwick, NSW Why this role matters: The Post-Doctoral Fellow will contribute to research projects within the UNSW-affiliated…

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python – Snakemake and github actions

The answer for any testing purpose is generally to put together a small and minimal dataset so the test completes in seconds or minutes while still being representative. It makes (to me) limited sense to have a Actions/CI running using for example the entire human genome as input. The point…

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Bioinformatics Engineer – Tufts University

Overview Tufts Technology Services (TTS) is a university-wide service organization committed to delivering technology solutions in support of Tufts’ mission of teaching, learning, research, innovation, and sustainability. With staff across all of Tufts’ campuses, as well as a 24×7 IT Service Desk, we collaborate with schools and divisions to meet…

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Bioinformatics Analyst III job with University of Florida

Bioinformatics Analyst III Job No: 526592Work Type: Staff Full-TimeLocation: Main Campus (Gainesville, FL)Categories: Biology/Life Science, Computer Science, Information Technology, Artificial Intelligence, Engineering, Physical/Mathematical SciencesDepartment: 29240101 – MD-HOBI-GENERAL Job Description Classification Title: Bioinformatics Analyst III Job Description: The Biomedical Informatics Program (BMI), hosted within the Department of Health Outcomes and Biomedical…

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GreenLight Biosciences hiring Bioinformatics Scientist (Crop Science) in Triangle, NC

About GreenlightAt GreenLight we are working to solve two of the world’s greatest problems: global food insecurity and equal access to vaccines and the associated health benefits. Unlike most corporations who can be required to put profits ahead of other principles, GreenLight is one of the first Public Benefit Corporations…

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Advisor/Sr. Advisor – Bioinformatics job in Cambridge at Lilly Company

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our 35,000 employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of…

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Pipeline Generator

Tool:Pipeline Generator 0 Hey everyone, We launched a new standalone service to help start the bioinformatics pipeline generation. It supports some popular pipelines like RNA-Seq, ATAC, scRNA, & CHiP and workflow managers like SLURM, Nextflow, & Snakemake. You can check it out here: ai.tinybio.cloud/pipeline-generator As always – feel free to…

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go_batch: A snakemake pipeline to assemble mitochondrial and ribosomal sequences from genome skims

Abstract Low coverage “genome-skims” are often used to assemble organelle genomes and ribosomal gene sequences for cost effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet degraded DNA often hinders PCR based analysis. However, with improvements to molecular techniques and sequencing technology, it is possible to…

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Error in snakemake with working shell script

Error in snakemake with working shell script 0 I want to run fastqc using snakemake. This is my snakemake script. configfile: ‘sample_config.yaml’ configfile: srcdir(‘path_config.yaml’) FASTQC = config[‘FASTQC’] UNZIP = config[‘UNZIP’] rule all: input: fqc1 = expand(“00_QC/{sample}_fastqc.txt”, sample = config[‘sample’]), rule fastqc: input: fq1 = lambda wildcards: config[‘sample’][wildcards.sample][‘fq1’], output: fqc1 =…

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Principal Scientist II Bioinformatics – Hiring Now at F. Hoffmann-La Roche Ltd in Mississauga, ON

We are searching for a persistent Principal Scientist II Bioinformatics to join our energetic team at F. Hoffmann-La Roche Ltd in Mississauga, ON.Growing your career as a Full Time Principal Scientist II Bioinformatics is an incredible opportunity to develop key skills.If you are strong in leadership, critical thinking and have…

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Moderna hiring Associate Bioinformatics Engineer in Cambridge, Massachusetts, United States

The RoleIn this role, you will develop computational protein engineering and bioinformatics pipelines and implement novel algorithms internally to support the Research and Early Development efforts for cancer vaccine related programs. You will work closely with computational scientists, bioinformaticians, statisticians, engineers and laboratory scientists within Oncology and cancer therapeutics teams…

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Scribe Therapeutics hiring Scientist II/Sr. Scientist, Bioinformatics in Alameda, CA

Scribe Therapeutics is a molecular engineering company focused on creating best-in-class in vivo therapies that permanently treat the underlying cause of disease. Founded by CRISPR inventors and leading molecular engineers Benjamin Oakes, Brett Staahl, David Savage, and Jennifer Doudna, Scribe is overcoming the limitations of current genome editing technologies by…

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Garvan Institute of Medical Research hiring Bioinformatics Research Assistant in Sydney, New South Wales, Australia

The Garvan Institute of Medical Research brings together world-leading clinicians and basic and translational researchers to break down barriers between traditional scientific disciplines and find solutions to disease. The Swarbrick lab are global leaders in the application of cellular genomics to human cancer, to find new diagnostics and treatments for…

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Data analyst in microbial bioinformatics (f/m/x)

The German Federal Institute for Risk Assessment (BfR) is the national institute which prepares expert reports and opinions on questions of food, feed and chemical safety and consumer health protection in Germany on the basis of internationally recognised scientific assessment criteria. It advises the Federal Government and other institutions and…

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Bioinformatics Engineer (Remote) @ Tufts University

Job:Bioinformatics Engineer (Remote) @ Tufts University 0 Overview jobs.tufts.edu/jobs/19311 Tufts Technology Services (TTS) is a university-wide service organization committed to delivering technology solutions in support of Tufts’ mission of teaching, learning, research, innovation, and sustainability. With staff across all of Tufts’ campuses, as well as a 24×7 IT Service Desk,…

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Bioinformatics Research Scientist, Division of Infectious Diseases and International Health – Charlottesville

The Division of Infectious Diseases and International Health is seeking a talented and passionate Bioinformatics Research Scientist to support ongoing bioinformatics analysis needs. The individual will integrate their knowledge and experience into current research and clinical efforts undertaken by two investigators, especially in analyzing large-scale genomic data with a focus…

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How to create a basic GUI for rna seq pipeline

Please do not reinvent the wheel – for your own sanity, because if you want to write that from the bottom up, you need a team of software engineers and at least (!) a year of time*. So rather check what is already out there in the Bioinfo world: Galaxy…

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Senior Computational Biologist / Sequence Bioinformatics

Senior Computational Biologist90% of drug candidates fail, delaying help for people in need. We’re on a mission to change that. Sequence Bio is a drug target discovery company. We are a committed team united in our purpose to discover the true signals of disease and accelerate the development of life-changing…

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Research Specialist IV – Bioinformatics at Sidra Medical and Research Center – Qatar

JOB SUMMARY  The Research Specialist IV – Bioinformatics performs routine and complex scientific work, evaluating, selecting and applying procedures and techniques to assignments with clear, specific objectives. Assignments require investigation of a number of variables and complex features.  Working with limited supervision, the role is required to exercise judgment in…

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Research Specialist IV – Bioinformatics – Career Growth Potential at Sidra Medical And Research Center in Qatar, Qatar

We are in search of an expert Research Specialist IV – Bioinformatics to join our innovative team at Sidra Medical and Research Center in Qatar, Qatar.Growing your career as a Full Time Research Specialist IV – Bioinformatics is a terrific opportunity to develop essential skills.If you are strong in creativity,…

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Bioinformatics Scientist II – Microbiome Center

SHIFT: Day (United States of America) Seeking Breakthrough Makers Children’s Hospital of Philadelphia (CHOP) offers countless ways to change lives. Our diverse community of more than 20,000 Breakthrough Makers will inspire you to pursue passions, develop expertise, and drive innovation. At CHOP, your experience is valued; your voice is heard;…

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Other jobs in San Diego, United States

Encodia is a proteomics platform company developing a new generation of single-molecule protein analysis tools. Our goal is to make proteome analysis easy and ubiquitous by converting peptide sequences into DNA barcode libraries that can be read by a DNA sequencer, providing a path to breakthrough proteomics research at scale….

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Bioinformatician/Sr. Bioinformatician, Functional Genomics Computation Unit job with Human Technopole

APPLICATION CLOSING DATE: 15th September 2023 Human Technopole (HT) is a new interdisciplinary life science research institute, created and supported by the Italian Government, with the aim of developing innovative strategies to improve human health. HT is composed of five Centers: Computational Biology, Structural Biology, Genomics, Neurogenomics and Health Data Science….

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Senior Bioinformatics Engineer – Sunnyvale

At Cepheid, we are passionate about improving health care through fast, accurate diagnostic testing. Our mission drives us, every moment of every day, as we develop scalable, groundbreaking solutions to solve the world’s most complex health challenges. Our associates are involved in every stage of molecular diagnostics, from ideation to…

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Problem with mamba/conda env create

Problem with mamba/conda env create 0 Hello everyone, I am new into this creating environment thing and not an expert in bioinformatics. So I do not know maybe this is a dumb question. I try to install packages, however I encountered with this warning message: Command: mamba env create –quiet…

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Snakemake excuting branching jobs

Snakemake excuting branching jobs 1 I want to apply different method to generate downstream file for same raw input, like: test.fq -> test_method_1.bam -> output_method_1.vcf -> downstream test.fq -> test_method_2.bam -> test_method_2.vcf -> downstream I can define two seperate sets of snakemake rules. However, the downstream analysing methods are same,…

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Bioinformatics Engineer job with Stanford University

Bioinformatics Engineer School of Medicine, Stanford, California, United States Information Analytics Post Date May 15, 2023 Requisition # 99140 The Department of Medicine,Division of Cardiovascular Medicineat Stanford University is seeking a talented Bioinformatics Engineer to join the Bioinformatics Core (BIC) of the Molecular Transducers of Physical Activity Consortium (MoTrPAC). As…

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Postdoctoral scientist: Bioinformatics for single-cell multi-omics

A postdoctoral position is available for a computational biologist at the Center of Human Genetics, KU Leuven in the team of Prof. Thierry Voet. In this position you will be responsible for the development and implementation of data analysis strategies for single-cell multi-omics data integration. You will then also be…

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Bioinformatics Analyst III Job in Florida

Classification Title: Bioinformatics Analyst III Job Description: The Biomedical Informatics Program (BMI), hosted within the Department of Health Outcomes and Biomedical Informatics (HOBI) and closely affiliated with the Clinical and Translational Science Institute (CTSI), engages in a wide variety of informatics research and service across the University of Florida….

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SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline

doi: 10.12688/f1000research.108835.2. eCollection 2022. Affiliations Expand Affiliation 1 Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA. Free PMC article Item in Clipboard John Krapohl et al. F1000Res. 2022. Free PMC article Show details Display options Display options Format AbstractPubMedPMID doi: 10.12688/f1000research.108835.2. eCollection 2022. Affiliation 1 Department…

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Bioinformatics Research Scientist, Division of Infectious Diseases and International Health job with Virginia Jobs

The Division of Infectious Diseases and International Health is seeking a talented and passionate Bioinformatics Research Scientist to support ongoing bioinformatics analysis needs. The individual will integrate their knowledge and experience into current research and clinical efforts undertaken by two investigators, especially in analyzing large-scale genomic data with a focus…

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Genomics Bioinformatics Software Engineer

Job details 21 July 2023 £49,592.00 to £58,769.00 per year £49592.00 – £58769.00 a year Full time 11 August 2023 London, NW9 5EQ NHS Jobs Contract K9919-23-0175 Apply for this job Summary The role is National and may involve travel to UKHSA locations in England for some meetings and site…

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Machine Learning Bioinformatics job with Rothamsted Research

Are you a talented Machine Learning Bioinformatician with a passion for advancing the field of bioinformatics? We are seeking a skilled individual to join our team working on an innovative discovery platform, known as KnetMiner. KnetMiner transforms the integration of genomics, genetics, literature information into comprehensive knowledge graphs, empowering researchers…

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Bioinformatics Engineer III in Philadelphia, Pennsylvania

SHIFT: Day (United States of America) Bioinformatics Engineer III – Children’s Hospital of Philadelphia (Philadelphia, PA): Lead the data integrity and bioinformatics data analysis of enterprise-level projects in the Center for Data-Driven Discovery in Biomedicine (D3b). Duties include: lead a bioinformatics data operational team responsible for the main bioinformatics analysis…

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Bioinformatics – Bethesda | Mendeley Careers

Job Description Overall Position Summary and Objectives Under this task order, the contractor will provide support services to satisfy the overall operational objectives. The primary objective is to provide services and deliverables through bioinformatics support services as part of an existing bioinformatics team. Minimum EducationMaster’s Resume Max Pages15 Certifications &…

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Bioinformatics Scientist job with Harvard University

62514BRAuto req ID:62514BRJob Code:RS0458 Bioinformaticist III Department Office Location:USA – MA – Cambridge Business Title:Bioinformatics ScientistSub-Unit:Sciences Salary Grade () :058Time Status:Full-time Union:00 – Non Union, Exempt or Temporary Basic Qualifications: Master’s degree in bioinformatics/computational biology or a related field with 5+ years of experience, or a PhD in bioinformatics, computational…

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Rstudio server in Snakemake

Rstudio server in Snakemake 0 Hello, I am new to using Snakemake and I am running a test script calling an R script. I work on a restricted server and I have access to a docker R studio server to run everything. However, it seems I am not able to…

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Fred Hutchinson Cancer Center (Fred Hutch) Bioinformatics Analyst II/III in Seattle, WA | 853342719

Minimum qualifications Master’s degree in bioinformatics, computational biology, biology, or related field with at least three years’ direct experience in computational analysis of large sequence-based molecular data sets. Fluency in at least one high-level programming language, such as Python, R, Ruby, JavaScript, or Perl Familiarity with version control and other…

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Roche hiring Bioinformatics Intern / Stagiaire en bio-informatique in Mississauga, Ontario, Canada

The PositionBioinformatics InternLength: 4 to 6 months.Type: Remote OR Hybrid.When you join us, you will have meaningful work developing an innovative technology that saves and improves lives around the world. As you collaborate with some of the best in the industry, you will make a huge difference in disease diagnostics!…

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