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snakemake snakemake

521

2.2k

mit

19

This is the development home of the workflow management system Snakemake. For general information, see

snakemake reproducibility workflow-management

Created 2019-10-04

5,197 commits to main branch, last one 2 days ago

RNA-seq-analysis crazyhottommy

292

849

mit

78

RNAseq analysis notes from Ming Tang

rna-seq snakemake

Created 2015-08-26

322 commits to master branch, last one 2 years ago

snakepipes maxplanck-ie

85

374

mit

19

Customizable workflows based on snakemake and python for the analysis of NGS data

ngs hi-c rna-seq atac-seq chip-seq workflow snakemake bisulfite-sequencing

Created 2016-03-23

3,817 commits to master branch, last one 2 months ago

atlas metagenome-atlas

100

355

bsd-3-clause

15

ATLAS - Three commands to start analyzing your metagenome data

assembly snakemake annotation metagenomics genomic-binning functional-annotation taxonomic-classifications

Created 2016-11-30

2,806 commits to main branch, last one 17 hours ago

rna-seq-star-deseq2 snakemake-workflows

194

315

mit

11

RNA-seq workflow using STAR and DESeq2

deseq2 snakemake sciworkflows reproducibility gene-expression-analysis

Created 2017-10-06

148 commits to master branch, last one 23 days ago

pypsa-eur PyPSA

207

305

unknown

16

PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System

pypsa energy snakemake energy-model energy-system power-systems energy-systems energy-system-model

Created 2017-10-11

4,833 commits to master branch, last one 8 days ago

multiPrime joybio

24

282

mit

15

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))

pcr tngs panel python viterbi snakemake multiplexpcr bioinformatics

Created 2022-09-05

332 commits to main branch, last one 2 months ago

dna-seq-gatk-variant-calling snakemake-workflows

141

233

mit

9

This Snakemake pipeline implements the GATK best-practices workflow

gatk snakemake sciworkflows reproducibility genomic-variant-calling

Created 2018-06-28

125 commits to main branch, last one 3 years ago

metaGEM franciscozorrilla

37

176

mit

5

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

mags snakemake metabolism microbiome metagenomics bioinformatics gut-microbiome systems-biology metabolic-models microbial-ecology metabolic-modeling computational-biology flux-balance-analysis genome-scale-metabolic-model metagenome-assembled-genomes

Created 2018-06-14

665 commits to master branch, last one 5 months ago

sunbeam sunbeam-labs

39

163

unknown

9

A robust, extensible metagenomics pipeline

snakemake metagenomics reproducible-research

Created 2016-04-28

1,727 commits to main branch, last one 8 days ago

docs snakemake-workflows

24

151

mit

14

Documentation of the Snakemake-Workflows project

snakemake snakemake-workflows

Created 2017-05-22

24 commits to master branch, last one 2 years ago

seq2science vanheeringen-lab

26

149

mit

6

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

ngs sra fastq rna-seq atac-seq chip-seq pipeline snakemake workflows bioinformatics reproducible-research bioinformatics-pipeline

Created 2019-07-11

1,483 commits to master branch, last one 4 months ago

dropSeqPipe Hoohm

46

146

cc-by-sa-4.0

9

A SingleCell RNASeq pre-processing snakemake workflow

umi plot star yaml conda picard dropseq multiqc scrbseq drop-seq pipeline scrb-seq snakemake dropseqtools reference-genome

Created 2016-08-02

333 commits to master branch, last one about a year ago

snakefmt snakemake

25

143

mit

6

The uncompromising Snakemake code formatter

fmt code black python formatter snakemake codeformatter bioinformatics

Created 2020-02-28

413 commits to master branch, last one 11 days ago

sequana sequana

27

141

bsd-3-clause

7

Sequana: a set of Snakemake NGS pipelines

ngs pacbio de-novo rna-seq coverage sequanix taxonomy snakemake variant-calling

Created 2016-03-07

6,337 commits to main branch, last one 3 months ago

V-pipe cbg-ethz

43

128

apache-2.0

10

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

hiv ngs conda virus genomics sarscov2 snakemake sars-cov-2 sequencing biohackeu20 biohackeu21 biohackeu22 biohackcovid20 bioinformatics bioinformatics-pipeline

Created 2017-04-10

1,170 commits to master branch, last one 15 hours ago

smk-simple-slurm jdblischak

14

120

cc0-1.0

7

A simple Snakemake profile for Slurm without --cluster-config

slurm snakemake bioinformatics snakemake-profile

Created 2021-05-01

59 commits to main branch, last one 8 days ago

sopa gustaveroussy

7

92

bsd-3-clause

6

Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells

pipeline snakemake spatialdata spatial-omics generalization memory-management multiplexed-imaging spatial-transcriptomics

Created 2023-09-04

767 commits to master branch, last one 17 days ago

dna-seq-varlociraptor snakemake-workflows

36

81

mit

8

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Var...

snakemake sciworkflows varlociraptor reproducibility genomic-variant-calling

Created 2020-01-17

393 commits to master branch, last one 8 days ago

grenepipe moiexpositoalonsolab

18

79

gpl-3.0

4

A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.

snakemake ancient-dna variant-calls pool-sequencing variant-calling snakemake-pipeline population-genetics evolve-and-resequence

Created 2020-05-06

530 commits to master branch, last one 3 months ago

sv-callers GooglingTheCancerGenome

34

73

apache-2.0

4

Snakemake-based workflow for detecting structural variants in genomic data

wgs workflow snakemake sv-calling bioinformatics cancer-genomics hpc-applications somatic-variants germline-variants structural-variants

Created 2017-04-10

474 commits to master branch, last one 4 months ago

tibanna 4dn-dcic

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70

mit

15

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ doc...