ufits v0.3.5

• minor fix to allow vsearch to work with older Ion Torrent Data where sometimes quality scores are greater than 41.

ufits v0.3.4

• added support for vsearch for pre-processing reads as well as mapping reads to OTUs. If vsearch is installed, scripts will use it automatically, otherwise default to Python and/or usearch
• fix bug in ufits filter that resulted in error if no index bleed filter or spike in barcode passed on argument line
• also a home-brew formula to install ufits. brew tap nextgenusfs/tap followed by brew install ufits will install the package as well as bedtools and vsearch two optional dependencies. usearch must still be installed manually.

ufits v0.3.3

• some bug fixes and updated docs
• fixed the local blast search for ufits taxonomy
• fixed ufits filter to work with any mock community fasta file
• update --uchime_ref to be able to use custom database
• fix logging in ufits database command

UFITS v0.3.2

A somewhat major bug fix: the de-multiplexing script for Ion Torrent data was not removing reverse primer correctly. This has been fixed.

• complete re-write of the ufits filter script to now normalize counts per number of reads in each sample prior to running the --index_bleed filter to remove noise from the dataset.
• ufits filter script now can deal with synthetic mock spike-in control (set as default). Calculates index-bleed in both directions and smartly filters OTU table. (email me for details on synthetic mock if you are interested).
• Taxonomy database was updated to most recent UNITE release
• Taxonomy database installation method is changed, now downloads pre-formatted databases for ITS1, ITS2, and FULL length ITS sets.
• Updated UCHIME reference sequences
• New functionality for ufits taxonomy that allows for removal of non-fungal OTUs with the --only_fungi argument
• Added script for sub-sampling or rarefaction of data prior to clustering
• Added script for selecting or removing samples from a de-mulitplexed data set
• Added script to append an OTU table to meta data file
• Added support for FUNGuilds functional annotation of taxonomy in OTU table.

ufits v0.2.8

• improvement of ufits database command for processing the taxonomy information for training UTAX
• added support for illumina data that is in a single file, i.e. with similar read setup as 454/ion ufits illumina2. I've seen this type of data from MrDNA service
• updated ufits install command to by default train UTAX for full length, ITS1, and ITS2 for ufits taxonomy
• minor bug improvements

ufits v0.2.6

• update to support Roche 454 reads (SFF or FASTA/QUAL as input) and need a fasta file of barcodes used
• minor bug fixes
• ufits install now skips primer trimming for UNITE+INSD database as it takes a lot of time without any added benefit because global search uses full length of the OTU and db doesn't matter if it is trimmed or not

ufits v0.2.5

• Several changes to syntax for commands to make easier to use.
• Added an install option to download, format, and create taxonomy databases from UNITE
• by default ufits taxonomy now uses a hybrid approach (UTAX and USEARCH) to get most out of taxonomy from legitimate hits. If USEARCH hit is < 97% identical, then UTAX is used. If hit is > 97% then taxonomy from UTAX vs USEARCH is compared and whichever result has more levels of taxonomy is used.

ufits v0.2.4

• minor bug fixes
• update to include ufits summarize command that generates taxonomy level OTU tables as well as makes a stacked Bar graph of each level of taxonomy in the dataset.

ufits v0.2.3

• update to allow for changing the UTAX confidence threshold for taxonomy (0 to 0.99), default is 0.8 or 80%

ufits.v0.2.1

• Major update that now supports taxonomy. You can assign taxonomy using the UTAX Classifier or using a more classical "blast" like search using USEARCH and a compatible database
• introduce ufits taxonomy, ufits download, and ufits database commands for assigning taxonomy
• several minor bug fixes