snakemake-workflow
There are 118 repositories under snakemake-workflow topic.
moiexpositoalonsolab/grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
4dn-dcic/tibanna
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.
felixleopoldo/benchpress
A Snakemake workflow to run and benchmark structure learning (a.k.a. causal discovery) algorithms for probabilistic graphical models.
lachlandeer/snakemake-econ-r
reproducible research project template for R using Renv and snakemake with an econ application
centrefornetzero/pypsa-fes
A model that optimises investment and operation, and incorporates flexibility domestic demand flexibility to model scenarios for Great Britain's future energy system.
laelbarlow/amoebae
Workflow for identifying and classifying homologous gene/protein sequences
metagenlab/MeSS
Snakemake pipeline for simulating shotgun metagenomic samples
sanjaynagi/rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
s-shemmee/s-shemmee
Config files for my GitHub profile.
NovembreLab/eems-around-the-world
Repo to analyze population genetic data with many different methods
guigolab/LyRic
Long RNA-seq analysis workflow
ylab-hi/ScanNeo2
Snakemake-based computational workflow for neoantigen prediction from diverse sources
fritzbayer/snakemake-with-R
Simple template for running snakemake with R
Serka-M/mmlong2-lite
Lightweight bioinformatics pipeline for microbial genome recovery
svsuresh/salmon_deseq2_snakemake
This repository has snakemake scripts for salmon-deseq2 pipeline for RNAseq data analysis
dohlee/snakemake-hamburger
:snake::hamburger: A beginner's guide to modular snakemake workflows.
mjmlab/pyinseq
Python pipeline for analyzing INSeq Insertion Sequencing data
RIVM-bioinformatics/SARS2seq
SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.
vibaotram/baseDmux
snakemake workflow for basecalling and demultiplexing of ONT sequencing data
allytrope/variant-analysis
A Snakemake pipeline for variant calling of genomic FASTQ data using GATK
chazeon/dpgen-snakemake
A lightweight Snakemake-based workflow that implements the DP-GEN scheme.
pyc1216/hlaloh-pipeline
hla-typing by optitype & polysolver , detect loh by lohhla.
RIVM-bioinformatics/ViroConstrictor
ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome
lachlandeer/angrist-krueger-1991
a small exercise using Angrist & Krueger's 1991 data in a reproducible workflow
niekwit/rna-seq-salmon-deseq2
Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2
open2c/distiller-sm
a Snakemake version of distiller - the Open2C Hi-C mapping workflow
thomasbtf/document-anonymization
Personal data redaction on images based on FHIR patient resources.
weigelworld/auto-asm
snakemake long read assembly pipeline
fischuu/Pipeline-Holoruminant-Meta
Easy to use Snakemake metagenomic pipeline that covers a) read-based analysis b) contig based analysis and c) MAG assembly and annotation using a broad set of ready to use and included public databases and annotators
insilicoconsulting/snake-chic
Snakemake wrapper around the Arima Capture Hi-C (CHiC) workflow
niekwit/crispr-screens
Snakemake workflow for CRISPR-Cas9 screen analysis
niekwit/cut_and_run
Snakemake workflow for Cut & Run
niekwit/damid-seq
Snakemake workflow for DamID-Seq analysis
niekwit/rna-seq-star-tetranscripts
Snakemake workflow for transposable element RNA-Seq using TEtranscripts
seqscope/NovaScope
The pipeline to process Novaseq dataset, from fastq to nge.