LotuS 2.24

Mostly cosmetic update, increasing readability of help function. Further added the option to add >1 custom reference databases.
Add the -intargetDB flag, to provide a list of amplicons that are kept in analysis and override all filtering parameters.

LotuS2 2.23

-new sdm version (2.23)
-improved help text (thanks Alastair)
-added new commandline options to control LCA id thresholds
-fixed LULU breaking, if only 1 sample was in dataset

LotuS2 2.22

Mostly a release to update sdm and some interface changes. sdm is now a bit faster, due to separating multithreading tasks better in the scheduler. This also makes sdm more stable in large datasets with lots of IO (ie -saveDemultiplex 1 on very large data).

• sdm v2.05
• LotuS2 v2.22

LotuS2 2.21

-fixed critical bug in dada2 clustering: when using "SequencingRun" column that was unsorted, recruited reads could be significantly lowered
-sdm v2.02: refactor code to make future work easier; slight speed increases
-new option "-mergePreClusterReads <1/0>" to merge reads before sequencing clustering. Not recommended currently, cluster quality seems to be lower when merging reads.
-various improved help texts

LotuS2 2.19

Some impossible flag configurations are caught now. Further added support for the latest DADA2 release in new R (>=4.1) version. removed minsize 5 parameter in unoise clustering.

LotuS2 2.17

small update to add sintax (==utax) and obtain a stable Zenodo doi

LotuS2 2.16

updated performance and precision
-CD-hit speed increased
-LCA retrieves significantly more species level hits at otherwise very similar performance
-interface cleaned up, shows more information now on chosen (partly automatic) parameters

2.14

-optimized PacBio HiFi amplicon seq mode (much faster now)
-included vsearch as a OTU clustering option
-changed backmapping to consistently minimap2 (increases overall speed)

LotuS 2.12

changed routine that backmaps mid-quality reads. This results on average in 5% more reads being used to estimate the abundances of taxa
increased derepMin to "8:1,4:2,3:3"
changed sdm default filter options (sdm_* files in configs folder) to filter harder reads not having fwd/rev reads, especially for PacBio and ITS related amplicon sequencing

2.11

-support for 2 barcodes on 1 read (e.g. in PacBio)
-made "CheckForMixedPairs" and "CheckForReversedSeqs" default in sdm_configs
-reworked detection of mixed-up (swapped) pairs and detecting reverse sequence by use of fwd primer detection (if fwd primer is not given, this will not be detected)
-ASVclustering algo beta version