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Top 15 snakemake open source projects

The uncompromising Snakemake code formatter

✭ 78

python Vim Script Makefile formatter fmt bioinformatics snakemake code black codeformatter

Documentation of the Snakemake-Workflows project

✭ 123

snakemake snakemake-workflows

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

✭ 17

c python shell rna-seq snakemake pipeline transcriptome mrna molecular-biology polya-tail

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/ docker), Snakemake (w/ conda) and custom Docker/shell command.

✭ 61

python HTML shell docker aws bioinformatics snakemake aws-lambda pipelines conda cwl aws-step-function wdl-workflow cwl-workflow snakemake-workflow

Close assembly gaps using long-reads at high accuracy.

✭ 39

d shell python docker bioinformatics snakemake cluster singularity dub pacbio genome-assembly daligner long-reads gap-filling close-assembly-gaps damapper

ATAC-seq snakemake pipeline

✭ 61

python shell snakemake atac-seq

🐍 Snakefiles for common RNA-seq data analysis workflows.

✭ 78

python shell bioinformatics rna-seq snakemake high-performance-computing lsf-jobs

Amplicon sequence processing workflow using QIIME 2 and Snakemake

✭ 23

python perl shell Dockerfile r snakemake dada2 deblur noaa-omics-software amplicon-sequence-variants

[MIRROR] Emacs support for Snakemake

✭ 30

emacs lisp Makefile snakemake

A robust, extensible metagenomics pipeline

✭ 143

python shell snakemake reproducible-research metagenomics

Exome/Capture/RNASeq Pipeline Implementation using snakemake

✭ 40

python perl r shell snakemake pipeline panel ngs tophat gatk rnaseq fastq exome ngs-pipeline annovar snpeff

rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

✭ 56

r python rna-seq snakemake reproducibility kallisto differential-expression sleuth sciworkflows

rna-seq-snakemake

Snakemake based pipeline for RNA-Seq analysis

✭ 29

r python PowerBuilder shell bioinformatics snakemake pipeline rna-seq-analysis rna-seq-snakemake

Monitor computational workflows in real time

✭ 45

CSS HTML javascript python bioinformatics snakemake reproducible-research workflows biohackeu20 biohackeu19

A workflow for creating small NGS test data sets, useful for continuous integration.

✭ 19

python snakemake ngs snakemake-workflows

1-15 of 15 snakemake projects