Results for "Snakemake"
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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
1740 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
2065 days ago
- Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless distribution of tasks over local or distribute...
Tags: Katuali, flexible, consensus, pipeline, Snakemake, basecall, assemble, polish, Oxford, Nanopore, Technology, sequencing, data
1924 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
1538 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
984 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
928 days ago
- This part of the documentation describes the snakemake executable. Snakemake is primarily a command-line tool, so the snakemake executable is the primary way to execute, debug, and visualize workflows. https://github.com/snakemake/snakemake/blob/main/docs/tutorial/bas...
Tags: Executing, Snakemake
581 days ago
