Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Toolkit for processing sequences in FASTA/Q formats

lumpy: a general probabilistic framework for structural variant discovery

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Finds SNP sites from a multi-FASTA alignment file

A tool set for short variant discovery in genetic sequence data.

Detecting sites of genomic enrichment

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency

Pairwise SNP distance matrix from a FASTA sequence alignment

A program to quickly count files in a subdirectory. This is mostly a programming demonstration.

A tool for bigWig files.

BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.

HMM-HDP models for MinION signal alignments

Scaffolding with RNA-seq read alignment