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

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

Utilities for representing and working with reference genomes

Stand-alone utility for filtering a BAM file to specific genomic regions, using Apache Spark.

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

Scala-focused OptionHandlers for args4j