v3.5.1

• Bug fix for creating dictionary of longest alignment lengths for each query read
• Accepts other sequence type options (Nanopore Q20:lr:hq, PacBio HiFi:map-hifi, traditional cDNA:splice:hq)
• Handles compressed (.gz) for output-unclassified
• forces minimap >=2.27

v3.5.0

Output "unclassified mapped" reads. Previously, all "unclassified" reads were only those that did not map with minimap2. This update now considers those as "unmapped" reads and additionally distinguishes "mapped unclassified reads". These reads are those that have only minimap2 mappings to species that are deemed not present in the sample, likely due to the overall community estimated abundance of the species being below the minimum abundance threshold.

This update also handles input fastas with read headers that are missing sequence data, #23.

v3.4.6

add --mm2-forward-only option