snakemake-workflows

snakemake-workflows/docs

Documentation of the Snakemake-Workflows project

snakemake-workflows/cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

Clinical-Genomics/BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

ctmrbio/stag-mwc

StaG Metagenomic Workflow Collaboration

snakemake-workflows/ngs-test-data

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

dohlee/snakemake-wrappers

:snake: Snakemake wrappers for bioinformatics.

signaturescience/metscale

MetScale: snakemake workflows to scale metagenome analyses

Alipe2021/NLncCirSmk

Pipeline for lncRNA, Circular RNA, and novel mRNA identification.

BIMSBbioinfo/crispr_DART

A workflow to analyse sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data

BIMSBbioinfo/pigx_scrnaseq

Pipeline for analysis of Dropseq single cell data

zhaoc1/nanoflow

Bioinformatics pipeline for nanopore sequencing data

Zilong-Li/lcWGS-imputation-workflow

Imputation workflow for low coverage whole genome sequencing data

hpc-carpentry/old-hpc-workflows

Scaling studies on high-performance clusters using Snakemake workflows

jlanga/smsk_trinotate

Snakemake workflow to run transdecoder + trinotate

hamidghaedi/pipeline_whole_exome_sequencing_analysis

The snakemake workflow for whole-exome sequencing analysis and generating vcf files

jlanga/smsk_popoolation

Snakemake pipeline for Popoolation and Popoolation2

DavideBrex/SpikeFlow

Pipeline to analyse ChIP-Rx data, i.e ChIP-Seq with reference exogenous genome spike-in normalization

zavolanlab/bindz-rbp

RBP module for bindz, a bioinformatics tool to detect regulators' binding sites on RNA sequences.

acesnik/LncRNADiscovery

Snakemake pipeline for lncRNA discovery and quantification

sandragodinhosilva/melange

Melange - Snakemake workflow for genome annotation

sk-sahu/Snakeflows

Collective Snakemake workflows for easy and reproducible NGS data analysis.

dohlee/snakemake-gatk

:snake::wrench: Snakemake wrappers for GATK.

crazyhottommy/pyflow-chromForest

snakemake workflow for random forest based feature selection on chromHMM data

hivlab/quantify-virome

quantify-virome: identify and quantify viruses from metagenomic shotgun sequences

LUMC/hutspot

Multisample DNAseq variant calling pipeline for use in diagnostics

mrmrwinter/asmapp

ASMAPP assembly appraisal workflow. Built in snakemake, ASMAPP performs many basic and intermediate assembly appraisal tasks.

pp4rs/2017-uzh-course-material

Repository that hosts the course materials for the 2017 edition of Programming Practices for Research in Economics at the University of Zurich

cbg-ethz/scdna-pipe

Python data analysis pipeline for single cell copy number event history reconstruction

mauriciolsfilho/mauriciolsfilho

Bem vido ao meu perfil

tdayris-perso/rna-dge-salmon-deseq2

Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2

tdayris-perso/vcf-annotate-snpeff-snpsift

Snakemake workflow designed to annotate VCF files withe SnpEff / SniSift

tdayris-perso/wes-mapping-bwa-gatk

Map and post-process your bams for SNP calling

XiaoqiLuo/whole_exome_squence_snakemake

Zilong-Li/array-imputation-workflow

imputation workflow for array data using shapeit2 and impute2

calliope-project/ec_modules

Make energy model workflows easy as 🥧!