Tag: SNAKEMAKE

Jobs on jobactive hiring Postdoctoral Bioinformatician in Single Cell and Spatial Omics Data Analysis in Adelaide, South Australia, Australia

Full-Time, 2 Year Contract Salary range $95,000 – $110,000 At the South Australian Health and Medical Research Institute (SAHMRI), we are committed to achieving innovative, ground-breaking health and medical research that fundamentally improves the quality of life for all people. The South Australian Genomics Centre (SAGC) is a multi-institutional, national…

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Associate Bioinformatics Scientist at Flagship Pioneering, Inc.

Company Summary: Who Are We? Founded by Flagship Pioneering, Empress pioneers the future of small molecule drugs through the discovery of pharmacologic loci. The company’s product platform leverages AI and multi’omic data from thousands of humans around the globe to discover novel, important small molecules inside of humans and their cognate mechanisms…

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Senior Research Associate/Principal Research Associate, Bioinformatics job with Vedanta Biosciences

Title: Senior Research Associate/Principal Research Associate, Bioinformatics Location: Cambridge, MA, or up to 100% remote Reports to: Scientist I, Bioinformatics The Role: We are looking for a bioinformatician/computational biologist to support the Research and Development team in the maintenance and querying of an existing laboratory information management system (LIMS), construction…

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Postdoc / Research Scientist in Bioinformatics and Computational Genomics

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

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UCSC and Amazon Web Services work to accelerate genomics research

The UC Santa Cruz Genomics Institute is collaborating with Amazon Web Services (AWS) to allow researchers to quickly and efficiently execute bioinformatics pipelines on AWS’s global cloud infrastructure. AWS and UCSC are committed to accelerating genomics research by integrating the Dockstore project, a leading repository for scientific and biomedical workflows…

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Push DaPars2 Docker image to APAeval Dockerhub

Following up on comments in PR review and #158, I need to push the Docker image to the APAeval instead of my personal account. It builds locally (and workflow works with it). 132341b425d1bbe0b1307bc50e8c0adcf1f7d68b on branch DaPars2-snakemake is the specific commit adding the Dockerfile (at execution_workflows/DaPars2/Dapars2_snakemake/workflow/envs/Dockerfile). @yuukiiwa @uniqueg could one of…

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Bioinformatics Application Scientist – Carlsbad

Job Description Bioinformatics Application Scientist (Actual title will depend on qualification and experience, including director level appointment) The Company: Universal Sequencing Technology Corporation (universalsequencing.com), a leading NGS biotechnology company engaged in long range/long read sequencing technology is relocating its headquarters from the greater Boston area to Carlsbad, CA where R&D…

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A Dynamic Snakemake Pipeline for Microbiome data analysis with QIIME2

%PDF-1.5 % 211 0 obj > endobj 295 0 obj >stream application/pdf Snaq: A Dynamic Snakemake Pipeline for Microbiome data analysis with QIIME2 2022-03-11T02:09:25Z LaTeX with hyperref 2022-03-13T05:02:28-07:00 2022-03-13T05:02:28-07:00 pdfTeX-1.40.23 False This is pdfTeX, Version 3.141592653-2.6-1.40.23 (TeX Live 2021) kpathsea version 6.3.3 uuid:4f5ae20a-1dd2-11b2-0a00-300927edca00 uuid:4f5ae20e-1dd2-11b2-0a00-380000000000 endstream endobj 212 0 obj > endobj…

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METASnake: a Snakemake workflow to facilitate…

Introduction As sequencing technology has become cheaper and more readily accessible, the need for the increased computational capacity to process these data has become apparent. In particular, high-throughput sequencing has been particularly useful when applied to the field of metagenomics. Substantial effort has been devoted to developing software and computational…

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Research Assistant, CSCB,LWK job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The SingHealth Duke-NUS Genomic Medicine Centre was established by SingHealth and Duke-NUS Medical School to advance the delivery of genomic medicine across the SingHealth Duke-NUS Academic Medical Centre (AMC). The Centre will bring together expertise from the various SingHealth institutions and Duke-NUS to leverage on advanced genomic technologies…

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Processing two lists of files with snakemake

I want to use snakemake to do bowtie2 mapping of split read files to a reference genome, and I’d like that rule to be integrated in the general workflow. For that purpose, I first defined a rule to create a bowtie index rule build_bowtie_index: input: referenceGenomeFasta output: expand(“{name}.{index}.bt2”, index=range(1,5), name…

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Bioconductor – AHLRBaseDbs

DOI: 10.18129/B9.bioc.AHLRBaseDbs     LRBaseDbs for AnnotationHub Bioconductor version: Release (3.14) Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the README.md of lrbase-workflow. Author: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido…

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Snakemake using multi inputs – Stackify

You need to define target output files using rule all. SAMPLES = [‘1’, ‘2’, ‘3’, ‘4’] rule all: input: expand(“sample{sample}.R{read_no}.fq.gz.out”, sample=SAMPLES, read_no=[‘1’, ‘2’]) rule fastp: input: reads1=”sample{sample}.R1.fq.gz”, reads2=”sample{sample}.R2.fq.gz” output: reads1out=”sample{sample}.R1.fq.gz.out”, reads2out=”sample{sample}.R2.fq.gz.out” shell: “fastp -i {input.reads1} -I {input.reads2} -o {output.reads1out} -O {output.reads2out}” This is the output of command snakemake -np, with…

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What do bioconda’s perl-net-ftp and perl-lwp-protocol-https do?

I was given some code of a previous intern and I’m supposed to find out what it does. It is a snakemake pipeline that has a my_pipeline.yaml file which is supposed to contain all the ‘general packages needed for the pipeline’ The file looks like this: name: my_pipeline channels: -…

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Assistant Professor of bioinformatics and ancient metagenomics – University of Copenhagen – job portal

Job Portal The GLOBE Institute at the Faculty of Health and Medical Sciences, University of Copenhagen seeks to appoint a temporary assistant professor of bioinformatics and ancient metagenomics to commence 1 May 2022 or soon as possible thereafter. Information on the department can be found at: ?url=https%3A%2F%2Fglobe.ku.dk&module=jobs&id=2223594″ target=”_blank” rel=”nofollow”>globe.ku.dk Job…

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python – Missing input files after defining them in function

I am trying to do QC on RNAseq data that is tarballed. I am using Snakemake as a workflow manager and am aware that Snakemake does not like one-to-many rules. I defining a checkpoint would fix the problem but when I run the script I get this this error message…

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Anyone know any clever snakemake/SLURM tricks to run a big analysis with limited storage?

Anyone know any clever snakemake/SLURM tricks to run a big analysis with limited storage? 1 I am using a SLURM HPC to run jobs and have ran into issues with storage. I have 3TB storage, and want to run over 1000 publicly available RNAseq data through my pipeline, which includes…

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snakemake truncating shell codes

snakemake truncating shell codes 0 I’m trying to change the chromosome number notation from [0-9XY] to Chr[0-9XY] using the samtools reheader in the shell command of the snakemake. rule rename: input: os.path.join(config[“input”], “{sample}.bam”), output: os.path.join(config[“output”], “new_sample/{sample}_chr.bam”) log: os.path.join(config[“log”], “samtools/{sample}”) shell: “samtools view -H {input} | sed -e ‘s/SN:([0-9XY]*)/SN:chr1/’ -e ‘s/SN:MT/SN:chrM/’…

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[moiexpositoalonsolab/grenepipe] freebayes causes early error about number of threads

Hi Lucas, got a weird one for you. If I change the caller from hapotypecaller to freebayes, I get the error below. It’s doubly strange because it seems to occur well before freebayes would be used in the pipeline. [Sat Dec 11 11:13:02 2021] rule samtools_stats: input: dedup/111D03-1.bam output: qc/samtools-stats/111D03-1.txt…

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Scripts for BGC analysis in large MAGs and results of their application to soil metagenomes within Chernevaya Taiga RSF-funded project

This repository include scripts for analysis of biosynthetic gene clusters (BGCs) in large metagenome assemblies. All scripts were created within the Chernevaya Taiga project funded by the Russian Science Foundation (grant 19-16-00049). The repository also contains results of the scripts application to four hybrid (illumina + ONT) assemblies of various…

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Aro Biotherapeutics hiring Investigator, Genetics & Bioinformatics in Philadelphia, Pennsylvania, United States

About Aro BioTx Join the team at Aro Biotherapeutics creating breakthrough biotherapeutics based on Centyrin oligonucleotide conjugates. Centyrins are small protein domains based on the fibronectin domains of human Tenascin C that combine the affinity and specificity properties of antibodies with the stability and tissue penetration properties of small molecules….

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iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

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Germline variant calling pipeline using Snakemake

Tool:Germline variant calling pipeline using Snakemake 0 Hello everybody, as part of a project, I had to write an in-house pipeline to call germline mutations for ~100 patients. For that I used Snakemake and GATKs best practice guidelines. Steps that take a long time (HaplotypeCaller or BaseQualityScoreRecalibration) are automatically parallelized…

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python – snakemake multiple parameters for multiple input and single output in snakemake. ConbineGVCFs gatk problem

I have written a rule for CombineGVCFs in gatk4. The rule is as follow all_gvcf = get_all_gvcf_list() rule cohort: input: all_gvcf_list = all_gvcf, ref=”/data/refgenome/hg38.fa”, interval_list = prefix+”/bedfiles/hg38.interval_list”, params: extra = “–variant”, output: prefix+”/vcf/cohort.g.vcf”, shell: “gatk CombineGVCFs -R {input.ref} {params.extra} {input.all_gvcf_list} -O {output} –tmp-dir=/data/tmp -L {input.interval_list}” all_gvcf is the dataset for…

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BIOINFORMATICIAN II

Apply at: uab.taleo.net/careersection/ext/jobdetail.ftl?job=T190159&tz=GMT-05%3A00&tzname=America%2FChicago A Bioinformatician II is needed to participate in research activities involved in the analysis of Next Generation Sequencing such as data derived from genomics and transcriptomics (bulk and single-cell sequencing) to the UAB Biological Data Science institutional core (www.uab.edu/cores/ircp/bds & Twitter page: twitter.com/UAB_BDS) . This position will…

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how to generate a file when snakemake pipeline failed

how to generate a file when snakemake pipeline failed 0 Hi there, I am working on a pipeline to make WES analyses. I am preparing that pipeline via snakemake. I have a problem about the input fasq file. Sometimes, users enter fastq files that are 8-9 mb. In this case,…

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Clinical Bioinformatics Scientist/Engineer Job in Massachusetts (MA), Career, Full Time Jobs in Novartis Pharmaceuticals

6500 – The number of associates in the Novartis Institutes for BioMedical Research (NIBR). This division is the innovation engine of Novartis, focusing on powerful new technologies that have the potential to help produce therapeutic breakthroughs for patients. We are seeking a bioinformatics scientist to coordinate the processing and…

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Pacific Biosciences hiring Bioinformatics Software Engineer in United States

PacBio’s Application Software Group focuses on building solid, strategic value around our core data type – highly accurate, long read sequencing – by producing innovative software that unlocks genomics in ways never seen before. We’re growing an interdisciplinary team of bioinformatic experts to tackle some of the most interesting problems…

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Research Scientist Bioinformatics at Exscientia

We are looking to hire an experienced bioinformatician who specializes in the analysis of human NGS data. The Research Scientist Bioinformatics will lead the development and expansion of our in-house NGS capabilities together with data managers and software developers, while also carrying out project-specific analyses. Exscientia GmbH is a company…

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Solvuu hiring Bioinformatics Engineer in United States

Summary At Solvuu, we are building technology to revolutionize bioinformatics and data science. We are seeking an accomplished, self-motivated and ambitious bioinformatics engineer with a strong track record in developing, executing, and maintaining bioinformatics pipelines on AWS for biotech R&D. The successful candidate will have the opportunity to drive and…

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Bioinformatics Engineer, Molecular Diagnostics Labs, UCLA Health

Job:Bioinformatics Engineer, Molecular Diagnostics Labs, UCLA Health 0 You will be part of a team of molecular biologists, medical geneticists, and bioinformaticians working together to analyze new and archival clinical cases using high throughput sequencing. As one of a newer team of software engineers, you will have the unique opportunity…

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Snakemake-Aligment using BWA-MEM2

Hello I have started using snakemake 6.5.2 to align fastq files with reference file. I have pasted the error below in this question. How to allocate memory in the snakefile and read the header from samfile, ‘-‘. This is the snakefile (wrapper for running alignment): rule bwa_mem2_mem: input: reads=[“/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.1.fq”, “/scicore/home/cichon/GROUP/test_workflow/samples/{sample}.2.fq”]…

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Head of Bioinformatics & Data Mining at HUMMINGBIRD BIOSCIENCE PTE. LTD. Singapore

About Hummingbird Bioscience Hummingbird Bioscience is an innovative clinical-stage biotech company focused on developing precision therapies against hard-to-drug targets to improve treatment outcomes. We harness the latest advances in systems biology and data science to better understand and solve the underlying causes of disease and guide development of our therapeutics. Enabled…

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Bioinformatics Software Engineer, Cancer Genomics Research Laboratory (req2036) job with Frederick National Laboratory

PROGRAM DESCRIPTION We are seeking an enthusiastic, creative, and collaborative bioinformatics software engineer to support pipeline development and analysis for our broad portfolio of genomic studies. If you have experience designing and deploying robust, reproducible, production-quality pipelines, then come join our talented team of bioinformaticians dedicated to understanding the genetics…

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