- update to Rscript running DADA2 to auto install the required R package if missing, this will only be done if package is missing - minor updates to output to terminal in `ufits dada2`
0.5.1
- new module to support DADA2 inferred sequences "clustering" method. Reads must be the same length, so may not be ideal for fungal ITS sequences (or other variable length amplicons). The script is run with `ufits dada2` and uses the output from any of the ufits pre-processing commands, i.e. `ufits ion`, `ufits illumina`, `ufits 454`, etc.
0.5.0
- update to `ufits cluster` to correctly output chimeras detected during clustering and reference filtering - update to automatically detect delimiters in parsing OTU tables - enhancement to allow for barcode mismatches in the `ufits illumina2` script - note the current implementation is slow and for 99% of uses I don't recommend setting barcode mismatches > 0.
0.4.9
- remove requirement of otu table for `ufits taxonomy` - add support for dual barcodes for `ufits illumina2` and `ufits 454` - default merge PE reads for `ufits illumina2` now rescues the forward reads if the pair cannot be merged
0.4.8
- fix bug in `ufits illumina` where period (.) where not processed correctly in sample names - fix bug in `ufits filter` when passing the `--cleanup` option. Totally dumb mistake.... - Add support for creating BIOM v2.1 OTU tables if you have the `biom` package installed. Also added a unified taxonomy 2-column output for each OTU. - added `--cleanup` option to `ufits illumina`
0.4.7
- fix for pre-processing reads from Illumina platform where custom sequencing primers are used, `ufits illumina` command now handles those datasets better. Note I would not recommend using custom primers, but that is of course up to you... - minor update to docs