Workflows
What is a Workflow?Filters
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
If you've ...
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.
The workflow takes a (trimmed) Long reads collection, runs Meryl to create a K-mer database, Genomescope2 to estimate genome properties and Smudgeplot to estimate ploidy (optional). The main results are K-mer database and genome profiling plots, tables, and values useful for downstream analysis. Default K-mer length and ploidy for Genomescope are 31 and 2, respectively.
Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.