Utilities for working with genomic bases, cigar strings, and phred scores.

Library for representing and working with sets of genomic-sequencing reads, e.g. BAM files.

Utilities for representing and working with reference genomes

Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework

Type-level & seamless command-line argument parsing for Scala

Unit-testing utilities