snakemake-pipeline

There are 5 repositories under snakemake-pipeline topic.

grenepipe
moiexpositoalonsolab / grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.
variant-calls snakemake snakemake-pipeline evolve-and-resequence population-genetics ancient-dna variant-calling pool-sequencing
Language:Python 79
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.
pipeline genomics nvidia-clara-parabricks nvidia-gpu snakemake-pipeline gatk4 gatk-bestpractices illumina exome-pipeline cohort-analysis
Language:Python 29
pmenzel / score-assemblies
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
genome-assembly genome-analysis bacterial-genome-analysis bioinformatics nanopore-assembly nanopore-sequencing snakemake-pipeline
Language:Python 23
pmenzel / ont-assembly-snake
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools
bacterial-genome-analysis bioinformatics nanopore-assembly nanopore-sequencing snakemake-pipeline
Language:Python 18
skchronicles / RNA-seek
A comprehensive quality-control and quantification RNA-seq pipeline
gene-expression gene-fusions quality-control rna-seq singularity snakemake-pipeline
Language:Python 10
brimittleman / apaQTL
Project for apaQTL MS. The workflowr project apaQTL by brimittleman
r python snakemake-pipeline genomics
Language:Shell 7
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.
vcf annotation-tool genomics bioinformatics-pipeline snakemake-pipeline
Language:Python 6
fritzbayer / snakemake-with-R
Simple template for running snakemake with R
r-workflow snakemake snakemake-pipeline snakemake-workflow
Language:R 6
OpenOmics / modr
An awesome Oxford Nanopore Pipeline for direct RNA-sequencing
direct-rna-sequencing oxford-nanopore rna-editing rna-modifications singularity snakemake-pipeline bioinformatics novel-transcripts pipeline quality-control transcriptomics known-transcripts polya-tail-length-estimation alternative-splicing-analysis differential-expression-analysis
Language:Python 6
smith-chem-wisc / Spritz
Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
bioinformatics proteogenomics snakemake snakemake-pipeline rna-seq proteomics
Language:C# 6
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
metagenomic-analysis metagenomic-pipeline metagenomics snakemake snakemake-pipeline
Language:Python 4
AngryMaciek / snakemake_suppa2
A snakemake workflow to perform Alternative Splicing analysis from RNA-Seq with SUPPA2.
snakemake-pipeline rna-seq alternative-splicing
Language:Python 3
CarolinaPB / population-structural-var-calling-smoove
population structural variant calling with smoove
bioinformatics pipeline snakemake snakemake-pipeline structural-variation structural-variation-calling smoove vep plink survivor
Language:Python 3
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.
hi-c hic hicexplorer snakemake snakemake-pipeline dchic selfish genova stripenn compartments loop tad
Language:Python 3
AngryMaciek / snakemake_fastqc
A small snakemake pipeline to perform quality analysis of RNA-Seq data with FastQC.
snakemake-pipeline rna-seq quality-control
Language:Python 1
CarolinaPB / snakemake-template
Template directory for creating a snakemake pipeline
bioinformatics snakemake snakemake-pipeline snakemake-tutorials
Language:Python 1
CarolinaPB / WUR_mapping-variant-calling
Short read mapping and variant calling
pipeline snakemake snakemake-pipeline short-reads mapping freebayes variant-calling
Language:Python 1
cmkobel / mspipeline1
🪆🦖 A snakemake wrapper around Nesvilab's FragPipe-CLI. In a perfect world, this pipeline was based on Sage.
fragpipe metaproteomics proteomics hpc parallel-computing snakemake-pipeline
Language:Python 1
fatmakahveci / milestone
bacterial strain identification
graph bacteria python snakemake strain bacterial-strain bacterial-genomes bioconda bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool conda snakemake-pipeline snakemake-workflow
Language:Python 1
raveancic / scRNAaltas_TNBC_mm
scrna-seq-analysis snakemake snakemake-pipeline cellranger singularity scrna pbs
Language:Python 1
svpipaliya / bulk-rnaseq
This repo contains scripts and workflows for performing bulk transcriptomics analyses
bioinformatics rna-seq snakemake-pipeline
Language:R 1
williamjeong2 / snakemake_RNA-seq
A repository for RNA-seq workflow
fpkm gene rna-seq-analysis rna-seq-data rna-seq-pipeline snakemake-pipeline snakemake-rna-seq
Language:R 1
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.
docker python reproducible-research research-object snakemake snakemake-pipeline snakemake-workflow
Language:HTML 0
AndreaMariani-AM / ChIPseq_snakemake
ChIPseq pipeline for Pasini's lab written in snakemake
bioinformatics-pipeline chip-seq chromatin computational-biology snakemake-pipeline
Language:Python 0
AndreaMariani-AM / CutNtag_snakemake
CutNtag pipeline for Pasini's lab written in snakemake
bioinformatics-pipeline computational-biology cutntag epigenetics snakemake-pipeline
Language:Python 0
AndreaMariani-AM / RNAseq_snakemake
RNAseq pipeline for Pasini's lab written in snakemake
bioinformatics-pipeline computational-biology rna-seq snakemake-pipeline transcriptomics
Language:R 0
CarolinaPB / population-mapping
Pipeline to map short reads from several samples to a reference genome
bioinformatics bioinformatics-pipeline mapping pipelines snakemake-pipeline
Language:Python 0
InstitutoTodosPelaSaude / respat
Pipeline for analyses of multiple pathogens, like SARS-CoV-2 with positivity rate analyses
influenza mamba python rsv sars-cov-2 sars-cov-2-variants snakemake snakemake-pipeline
Language:Python 0
michalbukowski / rnaseq-pipeline-1
Simple Snakemake RNA-Seq pipeline
bioconductor dge dge-analysis miniconda miniconda3 pandas python python3 r rna-seq rnaseq-analysis rnaseq-pipeline salmon salmon-deseq2 snakemake snakemake-pipeline snakemake-rna-seq
Language:Python 0
CarolinaPB / gbs-genetic-fitness
pipeline to perform gbs and genetic fitness analysis
gbs scaffolding bioinformatics pipeline snakemake snakemake-pipeline genotyping-by-sequencing
Language:Shell
dohlee / snakemake-hic-processing
Hi-C processing pipeline in snakemake.
bioinformatics hi-c pipeline reproducible-research snakemake snakemake-pipeline workflow
Language:Python
gauravcodepro / snakemake-iterations
utility for writing the snakemake files with faster iterations.
computing-cluster high-performance-computing snakemake snakemake-pipeline snakemake-pipelines snakemake-workflow
Language:Shell
ht-diva / meta_pipeline
meta-analysis metal snakemake snakemake-pipeline
Language:Python
Reina0101 / Python_dataprocessing_pipeline
Python & R multi-language data analysis pipeline
conda optimization python snakemake-pipeline demo
Language:R
Rendrick27 / AlignEvaluator
bioinformatics-pipeline python snakemake-pipeline
Language:Python
SammedMandape / NIST
Work at NIST: snakemake workflow to get short tandem repeats from WGS GIAB samples. R script for downstream processing and concordance
r snakemake-pipeline snakemake-workflow bioinformatics bioinformatics-pipeline
Language:R

snakemake-pipeline

moiexpositoalonsolab / grenepipe

ESR-NZ / human_genomics_pipeline

pmenzel / score-assemblies

pmenzel / ont-assembly-snake

skchronicles / RNA-seek

brimittleman / apaQTL

ESR-NZ / vcf_annotation_pipeline

fritzbayer / snakemake-with-R

OpenOmics / modr

smith-chem-wisc / Spritz

ac1513 / MAGqual

AngryMaciek / snakemake_suppa2

CarolinaPB / population-structural-var-calling-smoove

sebastian-gregoricchio / snHiC

AngryMaciek / snakemake_fastqc

CarolinaPB / snakemake-template

CarolinaPB / WUR_mapping-variant-calling

cmkobel / mspipeline1

fatmakahveci / milestone

raveancic / scRNAaltas_TNBC_mm

svpipaliya / bulk-rnaseq

williamjeong2 / snakemake_RNA-seq

aisaiahpellecer / is477-fall2023-final-project

AndreaMariani-AM / ChIPseq_snakemake

AndreaMariani-AM / CutNtag_snakemake

AndreaMariani-AM / RNAseq_snakemake

CarolinaPB / population-mapping

InstitutoTodosPelaSaude / respat

michalbukowski / rnaseq-pipeline-1

CarolinaPB / gbs-genetic-fitness

dohlee / snakemake-hic-processing

gauravcodepro / snakemake-iterations

ht-diva / meta_pipeline

Reina0101 / Python_dataprocessing_pipeline

Rendrick27 / AlignEvaluator

SammedMandape / NIST