Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework
Unit-testing utilities
Type-level & seamless command-line argument parsing for Scala
Scala-focused OptionHandlers for args4j
Library for representing and working with sets of genomic-sequencing reads, e.g. BAM files.
Utilities for working with genomic bases, cigar strings, and phred scores.