snakemake-workflow
There are 121 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
Scalable open-source software to run, develop, and benchmark causal discovery algorithms
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.
metagenlab/MeSS
Snakemake pipeline for simulating shotgun metagenomic samples
laelbarlow/amoebae
Workflow for identifying and classifying homologous gene/protein sequences
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.
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
ImagoXV/NanoASV
NanoASV official repo
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/crispr-screens
Snakemake workflow for CRISPR-Cas9 screen analysis
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
seqscope/NovaScope
The pipeline to process Novaseq dataset, from fastq to nge.
thomasbtf/document-anonymization
Personal data redaction on images based on FHIR patient resources.
weigelworld/auto-asm
snakemake long read assembly pipeline
Zhanglab-IOZ/TnpB
Snakemake workflows for TAM depletion analysis and de novo IS605 annotation
insilicoconsulting/snake-chic
Snakemake wrapper around the Arima Capture Hi-C (CHiC) workflow
niekwit/cut_and_run
Snakemake workflow for Cut & Run