snakemake-workflow

There are 142 repositories under snakemake-workflow topic.

  • grenepipe

    moiexpositoalonsolab/grenepipe

    A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.

    Language:Python10937224

  • felixleopoldo/benchpress

    Scalable open-source software to run, develop, and benchmark causal discovery algorithms

    Language:Python7344920

  • 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.

    Language:Python71137528

  • lachlandeer/snakemake-econ-r

    reproducible research project template for R using Renv and snakemake with an econ application

    Language:R632813

  • 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.

    Language:Python272122

  • metagenlab/MeSS

    Snakemake pipeline for simulating shotgun metagenomic samples

    Language:Python255153

  • laelbarlow/amoebae

    Workflow for identifying and classifying homologous gene/protein sequences

    Language:Python21212

  • guigolab/LyRic

    Long RNA-seq analysis workflow

    Language:Python20365

  • s-shemmee/s-shemmee

    Config files for my GitHub profile.

    191010

  • sanjaynagi/rna-seq-pop

    Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

    Language:Jupyter Notebook182819

  • tucca-cellag/tucca-rna-seq

    TUCCA's RNA-Seq Workflow for Read Quantification, Differential Expression, and Pathway Enrichment Analysis

    Language:R1812120

  • Serka-M/mmlong2-lite

    Lightweight bioinformatics pipeline for microbial genome recovery

    Language:Python17223

  • NovembreLab/eems-around-the-world

    Repo to analyze population genetic data with many different methods

    Language:R15518

  • ylab-hi/ScanNeo2

    Snakemake-based computational workflow for neoantigen prediction from diverse sources

    Language:Python143251

  • fritzbayer/snakemake-with-R

    Simple template for running snakemake with R

    Language:R12121

  • ImagoXV/NanoASV

    NanoASV official repo

    Language:Shell112494

  • mjmlab/pyinseq

    Python pipeline for analyzing INSeq Insertion Sequencing data

    Language:Python75416

  • niekwit/crispr-screens

    Snakemake workflow for CRISPR-Cas9 screen analysis

    Language:Python7231

  • svsuresh/salmon_deseq2_snakemake

    This repository has snakemake scripts for salmon-deseq2 pipeline for RNAseq data analysis

    Language:R7111

  • vibaotram/baseDmux

    snakemake workflow for basecalling and demultiplexing of ONT sequencing data

    Language:Python7311

  • dohlee/snakemake-hamburger

    :snake::hamburger: A beginner's guide to modular snakemake workflows.

    Language:Python6201

  • 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

    Language:HTML6380

  • pyc1216/hlaloh-pipeline

    hla-typing by optitype & polysolver , detect loh by lohhla.

    Language:R6121

  • 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.

    Language:Python6130

  • 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

    Language:Python6192

  • allytrope/variant-analysis

    A Snakemake pipeline for variant calling of genomic FASTQ data using GATK

    Language:Jupyter Notebook5100

  • chazeon/dpgen-snakemake

    A lightweight Snakemake-based workflow that implements the DP-GEN scheme.

    Language:Python5300

  • niekwit/rna-seq-salmon-deseq2

    Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2

    Language:Python5101

  • open2c/distiller-sm

    a Snakemake version of distiller - the Open2C Hi-C mapping workflow

    Language:Python56163

  • seqscope/NovaScope

    The pipeline to process Novaseq dataset, from fastq to nge.

    Language:Python5270

  • weigelworld/auto-asm

    snakemake long read assembly pipeline

    Language:Python5404

  • Zhanglab-IOZ/TnpB

    Snakemake workflows for TAM depletion analysis and de novo IS605 annotation

    Language:Python5133

  • EchoSingh/EchoSingh

    This repository serves as the foundation of my GitHub profile README, highlighting my projects, technical skills, and professional journey. It provides an overview of my contributions to open-source, personal projects, and areas of interest, while also reflecting my commitment to continuous learning and innovation.

    4103

  • MPUSP/snakemake-ont-basecalling

    A Snakemake workflow for basecalling and demultiplexing of Oxford Nanopore data using Dorado.

    Language:Python4

  • niekwit/gps-orfeome

    GPSW: A Snakemake workflow for GPS-ORFeome screens

    Language:Python40

  • Nirmal2310/ANOMALY

    Snakemake workflow for calling NUMTs from Long read sequencing data. The pipeline takes either FASTQ or BAM file and outputs a text file containing NUMTs.

    Language:Shell40