ufits v0.5.0

• 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.

ufits v0.4.9

• 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

ufits v0.4.8

• 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

ufits v0.4.7

• 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

ufits v0.4.6

• some bug fixes related to use of USEARCH9, UFITS now supports v9.0.2124 (note: do not use 9.0.2123 has error in -cluster_otus command)
• updates to how UFITS outputs the system info, now cleaner with more info on the OS
• fix bug on failed import for ufits keep and ufits remove

ufits v0.4.5

*bug fix in ufits taxonomy where would output csv file - this is only output tsv now

ufits v0.4.4

• bug fix related to downloading databases

ufits v0.4.3

• update to Databases: UNITE v7.1, LSU (based on RDP data), 16S (based on RDP gold), COI (based on BOLD database of arthropods and chordates).
• databases are installed now with ufits install -i ITS LSU 16S COI
• Robert Edgar now says that chimera reference filtering should use largest database (as opposed to UCHIME paper that says a small curated database is better), thus chimera reference filtering is now configured to do exactly that, options during clustering are: ufits cluster --uchime_ref [ITS,16S,LSU,COI, custom_path]
• ufits cluster_ref has been updated with the above database information - note this script is still experimental and I would not recommended using it for any environmental data at this point - there may be some targeted usage where it is appropriate
• re-write of ufits taxonomy to coincide with updates to databases, now you can pass one of the pre-installed databases to the -d, --db flag or you can specify manually a database using --fasta_db, --usearch_db, and/or --utax_db

ufits v0.4.2

• bug fix to ufits keep and ufits remove
• bug fix to ufits taxonomy where passing a --fasta_db failed
• update to README

ufits v0.4.1

• update to menu of ufits taxonomy to be more consistent with rest of the scripts, -i for input OTU table, -f for input fasta
• improve flexibility of ufits taxonomy to work with other groups, removed --only_fungi and replace with --tax_filter, i.e. --tax_filter Fungi.
• fix menu in wrapper scripts to reflect changes