Snakemake pipeline for simulating shotgun metagenomic samples
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Updated
Jul 26, 2024 - Python
Snakemake pipeline for simulating shotgun metagenomic samples
Align reads over a reference genome, filter aligned-reads, and mark duplicates
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
The pipeline to process Novaseq dataset, from fastq to nge.
Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon
Snakemake workflow for DamID-Seq analysis
Warlock is a snakemake workflow to spawn multiple demons (deme-based oncology models) as jobs running around on a cluster environment 😈😈
Snakemake workflow used to call peaks with Macs2
Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
A Snakemake workflow to run and benchmark structure learning (a.k.a. causal discovery) algorithms for probabilistic graphical models.
Pipeline for consensus prediction of cell types in single-cell RNA sequencing data.
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.
Download and index Ensembl sequences and annotations
Config files for my GitHub profile.
Snakemake-based computational workflow for neoantigen prediction from diverse sources
🦄 This repository contains all the best practices about GitHub
Snakemake file for handling concatenated Illumina .fastq.gz files to generate aligned sequence
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.
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
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