haowenz/chromap

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

Tools to process and analyze deep sequencing data.

Graph-based alignment (Hierarchical Graph FM index)

Tools for working with genomic and high throughput sequencing data.

ChIP-seq peak-calling, QC and differential analysis pipeline.

Analysis pipelines for genomic sequencing data

AdapterRemoval v3 - rapid adapter trimming, read merging, trimming, filtering, and QC

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome