Locityper  ◇  Targeted genotyping of complex loci using short and long reads [Rust].

ParascopyVC  ◇  Variant calling for duplicate regions [Python].

Parascopy  ◇  Paralog-specific copy number estimation for duplicated genes using short reads [Python].

Duplomap  ◇  Improving long-read alignment in segmental duplications [Rust].

Pileuppy  ◇  Colorful and fast BAM/CRAM pileup [Python].

iset  ◇  Rust library for interval trees, >315k downloads.

bam  ◇  Rust library for reading and writing BAM files, >26k downloads.