Workflows
What is a Workflow?Filters
This workflow supports processing of bulk ACT-Seq data from raw reads to genome-wide accessiblity tracks (bigWig) and ACT-Seq peaks. The main steps include read trimming using trimGalore, alignment with bowtie2, coverage generation using samtools and peak calling with MACS2.
This workflow supports processing of bulk CUT'N'RUN data from raw reads to genome-wide accessiblity tracks (bigWig) and CUT'N'RUN peaks. The main steps include read trimming using trimGalore, alignment with bowtie2, coverage generation using samtools and peak calling with MACS2.
This workflow supports primary processing of ChIP-Seq data from raw reads to genome-wide ChIP signal tracks and ChIP peaks. The main steps include read trimming using trimGalore, alignment with bowtie2, coverage generation using samtools and peak calling with MACS2.
This workflow supports processing of bulk ATAC-Seq data from raw reads to genome-wide accessiblity tracks (bigWig) and ATAC peaks. The main steps include read trimming using trimGalore, alignment with bowtie2, coverage generation using samtools and peak calling with MACS2.
GenErode pipeline
GitHub repository for GenErode, a Snakemake workflow for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
Documentation
The full pipeline documentation can be found on the repository wiki.
Citation
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A bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.