sourmash plugins
C++ and Python
Four sourmash plugins I wrote. dehash recovers the ACGT k-mers behind a signature, given the reads they came from. extract-errors finds the k-mers that appear exactly once across a pool of signatures, which are mostly sequencing errors, and emits them so they can be subtracted. subtract-and-inflate does that subtraction and restores abundances in one step. randsampling downsamples a signature to a fixed k-mer budget by abundance-weighted sampling.
I also contribute to two others: branchwater, sourmash’s multithreaded Rust plugin, where I added the pairwise and singlesketch subcommands, and commonhash, which filters hashes by how many sketches they appear in.
dehash ↗ extract-errors ↗ subtract-and-inflate ↗ randsampling ↗ branchwater ↗ commonhash ↗