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
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