Tag: HPC

Discovery Life Sciences hiring Bioinformatics Scientist in Huntsville, Alabama, United States

The Bioinformatics Scientist will take lab-generated data and create computational models that allow further manipulation and experimentation, perform incremental analysis required to process large amounts of data generated in a high-throughput Next Generation Sequencing (NGS) laboratory devoted to analysis of genomics data with a focus on long- and short-read sequencing…

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[slurm-users] Questions about scontrol reconfigure / reconfig

Hello, I have some questions about adding nodes in configless mode. My version of SLURM is 21.08.5. I gave logs below to ease the read of the message. First, is “scontrol reconfigure” equal to “scontrol reconfig” ? Then, I have a strange behaviour at node addition. I have an healthy…

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Job Opportunity: HPC Engineer at European Bioinformatics Institute (EMBL-EBI) (Hinxton, UK)

New Job opportunity posted by European Bioinformatics Institute (EMBL-EBI): We are seeking a HPC engineer to join our Compute team within our Technical Services Cluster (TSC), serving an institute of over 800 researchers and technical staff. You will be working closely with members of the department, and more widely with…

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MOLECULE package – LAMMPS Installation

Dear LAMMPS users, I want to run a LAMMPS simulation using HPC that include the Linux version of LAMMPS (14 Dec 2021), but I face the below error just after running the simulation: ERROR: Unrecognized atom style ‘full’ is part of the MOLECULE package which is not enabled in this…

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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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Postdoctoral Scholar – Bioinformatics/Biomedical Data Science

The University of Nevada, Reno (UNR) appreciates your interest in employment at our growing institution. We want your application process to go smoothly and quickly. Final applications must be submitted prior to the close of the recruitment. If you need assistance or have questions regarding the application process, please contact…

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How does slurm work? – IT & Software development Q&A

Hi, I was relatively recently told about slurm, however, as usual, I did not have time to go into details and had to quickly write scripts and subsample them “to not waste time”. Well, since recently, constantly goes out of timeout and scripts “do not finish” as simply not enough…

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Lightelligence’s optical processor is 100x faster than GPUs at math

Optical computing startup Lightelligence has developed a new GPU that outstrips the very best GPUs on the planet — at least in the most challenging mathematical problems — with the introduction of the Photonic Arithmetic Computing Engine (PACE). VIEW GALLERY – 2 IMAGES Lightelligence’s new Photonic Arithmetic Computing Engine (PACE)…

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Benchmarking the NVIDIA Clara Parabricks germline pipeline on AWS

This blog post was contributed by Ankit Sethia, PhD, and Timothy Harkins, PhD, at NVIDIA Parabricks, and Olivia Choudhury, PhD,  Sujaya Srinivasan, and Aniket Deshpande at AWS. This blog provides an overview of NVIDIA’s Clara Parabricks along with a guide on how to use Parabricks within the AWS Marketplace. It…

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[workshop] Building HPC clusters with LXD, Slurm & GPU:s – community-workshop

Welcome to join another exciting community workshop with Juju and related projects! This time @mmrezaie will take us through an interesting deployment of Slurm charms to build a HPC cluster with juju and lxd. Meeting link: meet.google.com/ceh-zber-jnf Date: Fri 2021-12-17 09:00 – 10:00 (UTC) Abstract In this workshop we will…

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A pandemic-scale phylogenetic analysis tool

Phylogenetics is an analytical tool that quickly analyzes genomic data to provide invaluable insights into the evolution and spread of a pathogen, thereby allowing public health officials and governments to respond to it in a timely fashion. During the coronavirus disease 2019 (COVID-19) pandemic, phylogenetics, like many other pre-pandemic tools,…

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16s rRNA Sequencing Meta-analysis Reconstruction Tool (using mothur).

16SMaRT is a bioinformatics analysis pipeline for 16s rRNA gene sequencing data. 16SMaRT is a “one-click” solution towards performing microbial community analysis of amplicon sequencing data. 16SMaRT aims to be your go-to solution for your next microbiome/metagenomics project. The primary objective of 16SMaRT analysis is to determine what genes are…

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Gaussian Fchk- What visualization programs? : comp_chem

I ran an HF calculation in Gaussian with the option formchk, and I’d like to take a look at the output orbitals. Usually I would use Gaussview, but our HPC system’s interactive desktop is down right now. The Gaussian documentation states:” formchk converts the data in a Gaussian checkpoint file…

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Postdoctoral Research Scientist, Bioinformatics – Turajlic lab job with The Francis Crick Institute

Reports to: Samra Turajlic [C] Job Description: Project summary An exciting opportunity to be part of a pioneering biomedical research institute, dedicated to innovation and science, in the laboratory of Samra Turajlic (Cancer Dynamics, www.crick.ac.uk/research/labs/samra-turajlic). We are seeking a highly collaborative and self-motivated post-doctoral bioinformatician to work within our comprehensive…

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Macbook Pro or PC laptop for bioinformatics?

Macbook Pro or PC laptop for bioinformatics? 3 I would like to be able to run most any of the typical ChIP-seq and RNA-seq tools (e.g. MACS2) from a home laptop computer; in other words, without access to HPC. I will be working with data from the relatively small eukaryotic…

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Unable to download fastq files in parallel / SOS

Unable to download fastq files in parallel / SOS 0 Hi! Very new to all this so bear with me if I’m using incorrect terminology. Also english is my second language. I’m trying to download my fastq files in parallel but it doesn’t work and I keep receiving this error:…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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Ensembl vep singularity

Ensembl vep singularity 0 Hello all, I would like to use variant effect prédictor on an hpc cluster. For that i use singularity with the docker image of vep : singularity pull –name vep.sif But i have a problem to use one plugin because a perl module is missing….

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Illumina hiring Bioinformatics Software Engineer 2 in San Diego, California, United States

Illumina’s Customer Collaboration & Innovation (CCI) team transforms the relationship between top-tier customers and our Product Development organization, and we are looking for a select individual to join the team as a Bioinformatics Software Engineer 2. The team works externally with a small number of Illumina’s top customers to design…

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POSTDOCTORAL FELLOW IN TRANSCRIPTOMICS AND BIOINFORMATICS

We are looking for an enthusiastic and ambitious postdoctoral fellow to study the pathophysiological bases of vascular anomalies via an integrated analysis of “omics” data (incl. single cell and bulk transcriptome, methylome, genome). The postdoctoral fellow will participate in all the omic aspects of the studies, from data analysis and…

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Bioinformatics Analyst – Job at NYU Grossman School of Medicine in New York, NY

is one of the nation’s top-ranked medical schools. For 175 years, NYU Grossman School of Medicine has trained thousands of physicians and scientists who have helped to shape the course of medical history and enrich the lives of countless people. An integral part of , the Grossman School of Medicine…

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Bioinformatics Software Engineer 2 in San Diego, California

Illumina’s Customer Collaboration & Innovation (CCI) team transforms the relationship between top-tier customers and our Product Development organization, and we are looking for a select individual to join the team as a Bioinformatics Software Engineer 2.  The team works externally with a small number of Illumina’s top customers to design…

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Suggestions for Alternate Assembly Resources to Trinity

Suggestions for Alternate Assembly Resources to Trinity 0 As far as I can tell, Galaxy no longer seems to support Trinity as an assembler – or at least, I have not been able to assemble any read data using Trinity for the past several months. Initially, I had had success…

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Bioinformatics Analyst 40%-60%, Zurich, fixed-term

Bioinformatics Analyst 40%-60%, Zurich, fixed-term 40%-60%, Zurich, fixed-term The ETH Zurich core facility NEXUS Personalized Health Technologies enables discovery and translational research for personalized health. We are recruiting a part-time Bioinformatics Analyst for the Clinical Bioinformatics Unit in Zurich to commence immediately or by mutual agreement. Job description The mission of…

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Principal Bioinformatics Scientist – Cell and Gene Therapy

Principal Bioinformatics Scientist – Cell and Gene Therapy Germany – Pharma The global Computational Biology and Digital Sciences (gCBDS) department is engaged in target discovery research and the application of innovative methods to resolve causative factors in disease progression. This is a great opportunity to lead computational projects in a…

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Invitae hiring Bioinformatics Scientist/Engineer in San Francisco, California, United States

Invitae is dedicated to bringing comprehensive genetic information into mainstream medicine to improve healthcare for billions of people. Our team is driven to make a difference for the patients we serve. We are leading the transformation of the genetics industry, by making genetic testing affordable and accessible for everyone to…

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Bioinformatician / Pipeline developer job with Paramount Recruitment

Bioinformatics / Pipeline Developer – Post DocCambridge This is a fantastic opportunity for a Post-Doc/PhD Graduate to join the R&D computational biology group as a Bioinformatics pipeline developer. This exciting company aim to transform the lives of cancer patients and their families through the development of precision treatments and ground-breaking…

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Bioinformatics Software Engineer I – Memorial Sloan Kettering Cancer Center

At Memorial Sloan Kettering (MSK), we’re not only changing the way we treat cancer, but also the way the world thinks about it. By working together and pushing forward with innovation and discovery, we’re driving excellence and improving outcomes.  We’re treating cancer, one patient at a time. Join us and make a…

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Bioinformatics Scientist 2 (Internal Only)

Job Summary We have an exciting opportunity in our US office for an experienced bioinformatician who is interested in working at the forefront of the gene editing (CRISPR knock-out, HDR, base editing) and gene modulation (CRISPRa, CRISPRi, RNAi) fields. As a Bioinformatics Scientist 2, you will have the opportunity to…

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Quest Diagnostics hiring Staff Scientist – Bioinformatics and Computational Biology in Marlborough, Massachusetts, United States

Look for more than answers.At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you can affect change…

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HaplotypeCaller Memory Optimization

HaplotypeCaller Memory Optimization 0 When using HaplotypeCaller on GATK, is there a fixed amount of memory that works well for for the java -Xmx input, or does it scale with the size of the input bam? eg if I have a 50 GB file do I need to set -Xmx…

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Job vacancy in Global Worldwide: Bioinformatics Engineer at SAIC

Job details Salary $125,001 – $135,000 a year job type full-time Full job description Job id: 2112092 Location: college park , md , us Date posted: 2021-08-12 Category: engineering and sciences Subcategory: systems engineer Schedule: full-time Shift: day job Travel: no Minimum clearance required: public trust Clearance level must be…

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Gromacs 4.5.4 manual

Gromacs 4.5.4 manual OntheStabilityofNegativelyChargedPlatelets inCalcium g_energy(1) [debian man page] Gromacs User Manual Version 4.6The defence of Königsberg had cost the lives of 42,000 German soldiers and 25,000 civilians. He yanked the seaman out and shouted at him to report straight to…

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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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Bioinformatics (HEO) Jobs in London at Public Health England –

The Bioinformatics and Whole Genome Sequencing (WGS) Software Development unit is part of Data Analytical Sciences within PHE’s National Infection Service Division. The unit is globally pre-eminent in the design, construction, validation and deployment of bioinformatics pipelines for the automated analysis of Next Generation Sequencing (NGS) whole Genome Sequence (WGS)…

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Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

1. Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5. CAS  PubMed  PubMed Central  Article  Google Scholar  2. Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72. PubMed  Article  PubMed Central  Google Scholar  3. Borrel G, McCann A, Deane J, Neto…

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Bioinformatics Analyst I – Job at Medical College of Wisconsin in Milwaukee, WI

Position Description: Every great life-changing discovery begins the same way-with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do…

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Bioinformatics Scientist in Frederick, MD

Job DescriptionBioinformatics ScientistFull Time Direct Hire Remote positionAre you looking for bioinformatics work? Are you interested in joining a team of talented bioinformaticians dedicated to understanding the genetics of cancer? In this role you will:* Function as a scientific thought leader within for all aspects of GWAS and population genetics….

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Bioinformatics Pipeline Developer job in Cambridge, Cambridge

Job Information Role Overview We are currently looking for a Bioinformatics Pipeline Developer to join a leading Biotech company based in the Cambridgeshire area. As the Bioinformatics Pipeline Developer you will be working on early cancer detection technology by supporting software developers and bioinformaticians Key Duties and Responsibilities 1. The…

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REMOTE Bioinformatics Research Associate – The Planet Group

JOB DESCRIPTION: The Human Genetics Department is currently offering an temporary employee position for students or working professionals in Bioinformatics/Computational Biology to join its Bioinformatics Team. The successful candidate will be actively engaged in mining the human genetics and genomics data to identify and prioritize targets. The successful candidate will be…

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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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Research Fellow / Senior Research Assistant (Bioinformatics) at Northumbria University

Northumbria University is a member of the COVID-19 Genomics UK Consortium (COG-UK).  COG-UK is a pioneer in the use of large-scale, rapid whole-genome sequencing of SARS-CoV-2, the virus causing the COVID-19 pandemic, to understand viral transmission and evolution, and to inform public health responses and vaccine development. We seeking to…

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Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance

1. Lee, M.-R. et al. Mycobacterium abscessus complex infections in humans. Emerg. Infect. Dis. 21, 1638–1646 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Prince, D. S. et al. Infection with Mycobacterium avium complex in patients without predisposing conditions. N. Engl. J. Med. 321, 863–868 (1989). CAS  PubMed  Article  Google…

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Head of Bioinformatics job in Princeton, NJ | GENMAB A/S

Genmab is focused on the creation and development of innovative and differentiated antibody products, with the aim of improving the lives of cancer patients. The Role The successful candidate will lead the global bioinformatics function and be responsible for many aspects of data including architecture, access, classification, standards, integration, pipelines…

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Senior Research Associate in Bioinformatics job with University of Bristol

The role We are looking for an experienced bioinformatician to provide support for academic users of the University of Bristol Genomics facility and to teach on our Bioinformatics Masters course. What will you be doing? The role holder will be working as part of the Genomics Facility team, a core…

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Asuragen hiring Advanced/ Senior Bioinformatics Analyst in Austin, Texas, United States

The Opportunity Asuragen, a Bio-Techne brand, is a global molecular diagnostics product and solutions company, and we use our unique combination of proprietary chemistry and bioinformatics to develop products that address unmet needs for both clinical research and diagnostic laboratories. Our product portfolio is comprised of reagent kits and software…

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Bioinformatics Software Engineer | Novartis United States of America

You will have: • B.S./M.S. in Computer Science or Bioinformatics, with 2-4 years of related professional experience• Domain knowledge in bioinformatics and experience in working with omics data• Experience with a combination of Python, R• Experience working in Linux environment and proven knowledge of Linux command line utilities• Experience with…

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Bioinformatics Analyst in Pittsburgh, PA

Description Purpose: The UPMC Genome Center is a clinical grade, full-service, high-throughput genome center with sequencing options designed for both clinical and research needs. We are looking for members to join our Bioinformatics team for analysis of a wide spectrum (Whole Exome/Genome Germline and Somatic, RNAseq, scRNAseq) of NGS data…

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HPC Engineer at European Molecular Biology Laboratory (EMBL)

About the team/job We are seeking a HPC engineer to join our Compute team within our Technical Services Cluster (TSC), serving an institute of over 800 researchers and technical staff. You will be working closely with members of the department, and more widely with technical users across EMBL-EBI, playing an…

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Novartis Institutes for BioMedical Research (NIBR) hiring Bioinformatics Software Engineer in Cambridge, Massachusetts, United States

Job Description6,000 people dedicated to discovery – 6 research campuses across the globe – 1 purpose…to reimagine medicine! Novartis Institutes for BioMedical Research (NIBR) 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…

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REditools2 (HPC-reditools) de-novo editing prediction from RNAseq?

I am having some trouble with REditools2 (HPC-Reditools). In the original version of reditools there was a python script for de-novo prediction of editing sites from RNAseq data using a strategy outlined in Picardi et al 2012. I assumed reditools2 would have this same feature. However, after inputting the appropriate…

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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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In KisSplice, I already set “ulimit -s unlimited”, but I am still getting stack limit error. Is there a work around this?

In KisSplice, I already set “ulimit -s unlimited”, but I am still getting stack limit error. Is there a work around this? 1 Objective: I am trying to use kissplice to obtain SNPs from my RNA-seq (fastq) data. Problem: Even after setting the stack limit to unlimited, I am still…

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Senior Programmer Analyst/Bioinformatics in New York, NY for Columbia University

  Job Seekers, Welcome to HERC Jobs Senior Programmer Analyst/Bioinformatics Columbia University Columbia University Job Type: Officer of Administration Bargaining Unit: Regular/Temporary: Regular End Date if Temporary: Hours Per Week: 35 Salary Range: Commensurate with experience  …

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Bioinformatician – Gene Expression Team job with EMBL

The Gene Expression Team analyses expression data sets at tissue or single cell level and develops Expression Atlas, a resource that provides information about the expression of genes and proteins in different cells, tissues, developmental stages and conditions. Your role We are looking for a data production service bioinformatician to…

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IT System Engineer at European Molecular Biology Laboratory (EMBL)

About the team/job EMBL is Europe’s flagship research organization for the life sciences – an intergovernmental organization with more than 80 independent research groups covering the spectrum of molecular biology. EMBL is international, innovative and interdisciplinary – its approx. 2000 employees of more than 80 nationalities, operate across six sites…

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Error when Phasing with Beagle 5.2

Error when Phasing with Beagle 5.2 0 I’m having trouble phasing a multi-sample (9-samples) vcf file produced by gatk HaplotypeCaller with Beagle 5.2. I do not have a genetic map or reference panel. I am working with a very heterozygous group of organisms (sea urchins). When I run beagle with…

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BUSCO installation and run

BUSCO installation and run 2 That unil.ch link looks a bit too complicated, these are the commands I ran to get BUSCO via Singularity: Download the image: singularity pull Run the image with example genome.fasta, assuming it’s a genome and a plant: singularity run -B $(pwd):/busco_wd/ busco_v5.2.2_cv1.sif busco -l…

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