snakemake-pipeline
There are 44 repositories under snakemake-pipeline topic.
ESR-NZ/human_genomics_pipeline
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
LaborBerlin/score-assemblies
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
ac1513/MAGqual
MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards
skchronicles/RNA-seek
A comprehensive quality-control and quantification RNA-seq pipeline
fritzbayer/snakemake-with-R
Simple template for running snakemake with R
ESR-NZ/vcf_annotation_pipeline
A Snakemake workflow to filter, annotate and prepare variant call format (VCF) data for scout using GATK4, SnpSift, VEP and genmod. Designed to be used after human_genomics_pipeline.
brimittleman/apaQTL
Project for apaQTL MS. The workflowr project apaQTL by brimittleman
smith-chem-wisc/Spritz
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
OpenOmics/modr
An awesome Oxford Nanopore Pipeline for direct RNA-sequencing
open2c/distiller-sm
a Snakemake version of distiller - the Open2C Hi-C mapping workflow
AngryMaciek/snakemake_suppa2
A snakemake workflow to perform Alternative Splicing analysis from RNA-Seq with SUPPA2.
CarolinaPB/population-structural-var-calling-smoove
population structural variant calling with smoove
sebastian-gregoricchio/snHiC
Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.
AngryMaciek/snakemake_fastqc
A small snakemake pipeline to perform quality analysis of RNA-Seq data with FastQC.
CarolinaPB/gbs-genetic-fitness
pipeline to perform gbs and genetic fitness analysis
CarolinaPB/snakemake-template
Template directory for creating a snakemake pipeline
CarolinaPB/WUR_mapping-variant-calling
Short read mapping and variant calling
cmkobel/mspipeline1
🪆🦖 A snakemake wrapper around Nesvilab's FragPipe-CLI. In a perfect world, this pipeline was based on Sage.
Moha-cm/AutoRNASeq
Simplified RNA-Seq Insights with automation
svpipaliya/bulk-rnaseq
This repo contains scripts and workflows for performing bulk transcriptomics analyses
williamjeong2/snakemake_RNA-seq
A repository for RNA-seq workflow
aisaiahpellecer/is477-fall2023-final-project
Final project submission for IS477 course at University of Illinois Urbana-Champaign. Utilized Snakemake for efficient creation of research objects, applying semester's knowledge on data curation, management, and reproducibility.
AndreaMariani-AM/ChIPseq_snakemake
ChIPseq pipeline for Pasini's lab written in snakemake
AndreaMariani-AM/CutNtag_snakemake
CutNtag pipeline for Pasini's lab written in snakemake
AndreaMariani-AM/RNAseq_snakemake
RNAseq pipeline for Pasini's lab written in snakemake
hermidalc/tcga-wgs-kraken-microbial-quant
Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS data
InstitutoTodosPelaSaude/respat_snakemake
Pipeline for analyses of multiple pathogens, like SARS-CoV-2 with positivity rate analyses
michalbukowski/rnaseq-pipeline-1
Simple Snakemake RNA-Seq pipeline
Reynaaaaaaaaaaa/Python_dataprocessing_pipeline
Python & R multi-language data analysis pipeline
codecreatede/snakemake-utility
bash based utility for writing the snakemake iteration
dohlee/snakemake-hic-processing
Hi-C processing pipeline in snakemake.
Programa-de-neoplasias-linfoides/rnaseq_virginia
RNASeq Pipeline for Virginia Amador group
SammedMandape/NIST
Work at NIST: snakemake workflow to get short tandem repeats from WGS GIAB samples. R script for downstream processing and concordance