Results for "Workflow"

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  • Taverna Workflow Management System

    Taverna is an open source domain independent Workflow Management System – a suite of tools used to design and execute scientific workflows. Taverna has been created by the myGrid project and is funded through a range of organisations and projects. The Taverna suite is written in Java and i...

    Tags: Bioinformatics, Computational Biology, Management, Workflow

    3878 days ago

  • Swabs to Genomes: A Comprehensive Workflow

    The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library pr...

    Tags: Bioinformatics, Computational Biology, Workflow, Genome, Commands

    3519 days ago

  • COSMOS, our workflow management system for NGS data

    COSMOS, our Python-based management system for implementing large-scale parallel workflows focusing on, but not restricted to, large-scale short-read "NGS" sequencing data is open-access published via Advance Access in Bioinformatics (Gafni et al. 2014).  It is also available for download fo...

    Tags: Bioinformatics, Computational Biology, NGS, COSMOS, Python, Workflow

    3537 days ago

  • WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.

    Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community metagenomes remains an open problem. To address this, we ...

    Tags: WAAFLE, Workflow, Annotate, Assemblies, Find, LGT, Events

    917 days ago

  • MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales

    This tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detectio...

    Tags: MimiLook, Phylogenetic, Workflow, Detection, Gene, Acquisition, Major, Orthologous, Groups, Megavirales

    809 days ago

  • CLAW: Chloroplast Long-read Assembly Workflow

    CLAW (Chloroplast Long-read Assembly Workflow) is an mostly-automated Snakemake-based workflow for the assembly of chloroplast genomes. CLAW uses chloroplast long-reads, which are baited out of larger read libraries (e.g., an Oxford Nanopore Technologies MinION read library derived from photosynt...

    Tags: CLAW, Chloroplast, Long-read, Assembly, Workflow

    36 days ago

  • Snakemake workflow: dna-seq-gatk-variant-calling

    This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.

    Tags: Snakemake, workflow, dna-seq-gatk-variant-calling, snp

    1708 days ago

  • Snakemake—a scalable bioinformatics workflow engine

    Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. 

    Tags: Snakemake, scalable, bioinformatics, workflow, engine

    2034 days ago

  • VirtualFlow: a versatile, parallel workflow platform for carrying out virtual screening

     related tasks on Linux-based computer clusters of any type and size which are managed by a batchsystem (such as SLURM).  Currently, there exist two versions of VirtualFlow, which are tailored to different types of tasks: VFLP: VirtualFlow for Ligand Preparation VFVS :&nb...

    Tags: VirtualFlow, versatile, parallel, workflow, platform, carrying, virtual, screening

    1384 days ago

  • RNA-seq workflow: gene-level exploratory analysis and differential expression

    Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count datasets for downstream analysis. We will perform explo...

    Tags: RNA-seq, workflow, gene-level, exploratory, analysis, differential, expression

    902 days ago