v2.34.1

minor changes to autoinstaller

LotuS2 2.34

small update adding

• AVITI support
• suppressed LULU warning
• usearch12 added by default for autoinstaller

LotuS2 2.32

small fix for

• lambda3 DB built
• copying RDP classifier files

LotuS2 2.31

small update to download lambda indexes for LotuS2 conda built
bugfixes:

• hitDB file suffix renamed to work with lambda3

LotuS2 2.30

LotuS2 2.30:

• lambda3 instead of lambda: massive speedups in tax assignments, using less ram (thanks to https://github.com/seqan/lambda)
• UNITE v9. While this database is more up to date, in general users reported less species level fungal assignments in LCA assignments. This could be due to "splitting" of species into independent species in v9, but we'll keep an eye on the situation
• updated a bit autoInstaller interface, LotuS2 program logic
• fixes in README

LotuS2 2.28.1

Small update to include updated sdm 2.14

Lotus2.28

small update focused on:

• clearer interface
• autoInstall changes related to conda install

LotuS2 2.27

In this update new reference databases were added, and the -taxOnly functionality cleaned up.

• added KSGP SSU database following a GTDB tax (https://www.biorxiv.org/content/10.1101/2023.08.21.554127v1)
• added GreenGenes2 (GG2) SSU database following a GTDB tax
• "-taxOnly works substantially cleaner, requiring less side arguments, clearer reporting
• automatically produces "LotuSLogS/LCAhits.log" file that will list the distribution of best hits (similar to Fig. 1 KSGP analysis https://www.biorxiv.org/content/10.1101/2023.08.21.554127v1)

LotuS2 2.26

• updated PacBio CCS amplicon documentation
• reworked PacBio CCS amplicon clean up steps - much stricter, but also much better

LotuS 2.25

Small update that changes default ASV behaviour and backmapping