Second Major Version: Updated Rust-Bio data structures. This includes a sampled suffix array which reduces the size of the MG-Indices. Indices built with different major versions will not be compatible. New output format. The binning output now reports the alignment edit distance for hits. The collapse command works with this new output and will not be compatible with previous output format New inputs allowed. The binning command now accepts either FASTA or FASTQ format inputs. The queries no longer need to be the same size. Parameter changes To account for different size queries, the binning parameters have been modified. The edit distance is now a proportion (--edit-rate) based on the length of the read. The --seed-gap parameter was renamed --seed-interval to be more consistent with other tools. The minimum seed threshold (--min-seed) is now a percentage of the number of seeds to allow different size reads. What's Changed Dev by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/1 build FM-index from ssa references by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/2 Dev by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/3 Dev by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/4 Update tests by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/5 update stopwatch by @tfursten in https://github.com/FofanovLab/mtsv_tools/pull/6 Full Changelog: https://github.com/FofanovLab/mtsv_tools/compare/1.0.2...2.0.0