Snakemake pipeline for simulating shotgun metagenomic samples
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Updated
Sep 7, 2024 - Python
Snakemake pipeline for simulating shotgun metagenomic samples
Snakemake workflow for DamID-Seq analysis
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Align reads over a reference genome, filter aligned-reads, and mark duplicates
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Snakemake workflow used to call peaks with Macs2
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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.
Download and index Ensembl sequences and annotations
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.
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