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
1745 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
2071 days ago
Tags: Katuali, flexible, consensus, pipeline, Snakemake, basecall, assemble, polish, Oxford, Nanopore, Technology, sequencing, data
1929 days ago
Sequanix: a dynamic graphical interface for Snakemake workflows
A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats). A set of pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework) with more than 80 re-usable rules (see Rules). Original tools to help in th...Tags: Sequanix, dynamic, graphical, interface, Snakemake, workflows
1543 days ago
The Snakemake Wrappers repository
The Snakemake Wrapper Repository is a collection of reusable wrappers that allow to quickly use popular tools from Snakemake rules and workflows. More at https://github.com/snakemake/snakemake-wrappersTags: Snakemake, Wrapper, Repository, collection, reusable, wrappers, package
989 days ago
Basic Structure of Snakemake Pipeline Run !
/user/snakemake-demo$ ls config.json data envs scripts slurm-240702.out Snakefile data = mock data for the snakefile to use Snakefile = name of the snakemake “formula” file Note: The default file that snakemake looks for in the current working directory is the Snakefile. ...Tags: Snakemake, Pipeline, Flow, Learn
933 days ago
Tags: Executing, Snakemake
587 days ago