ufits v0.7.1

• bug fix in ufits illumina where R2 reads were not getting trimmed correctly.

ufits v0.7.0

I bumped versions here to illustrate that UFITS has changed a little under the hood, now requires at least USEARCH v9.1.13 and requires at least VSEARCH v2.20. These changes were made to maximize speed and simplify the code. The scripts will terminate if they detect lower versions of both of these software tools. BIOM, RDP, Blast are still "soft dependencies".

• bug fix in ufits taxonomy where RDP taxonomy was not processed correctly for BIOM conversion
• fix for #14
• fix for #13 by moving to VSEARCH for this task
• fix for #12, now ufits filter requires you to add a mock community fasta file --mc if you specify a -b, --barcode to filter your data on
• fix for ufits filter to deal with OTU tables that have taxonomy already appended
• fix for ufits cluster_ref where script would die after conversion to VSEARCH as hard dependency
• re-write of ufits heatmap to have a few more options and more flexibility.
• update to docs as well as a section showing how to get your data into downstream statistical tools

ufits v0.6.1

• bug fix in ufits taxonomy if --tax_filter was used the filtered OTU table would not be correct in the BIOM output file
• fix for ufits ion if using --mult_samples now creates mapping_file correctly.
• updates to the docs on new usage

ufits v0.6.0

Several major changes in this version:

• taxonomy for ITS is updated to newest release from UNITE v7.1 11-20-2016.
• USEARCH9 is now supported throughout and defaults have been changed to use usearch9
• UNOISE2 algorithm is employed in a 'clustering' module
• SINTAX algorithm is supported in ufits taxonomy. default hybrid method now uses SINTAX, UTAX, and global alignment to infer the best taxonomy assignment.
• QIIME-like mapping files can now be used during demultiplexing/pre-processing. If you do not use a mapping file, the scripts will create one for you. The mapping file can be used to add metadata to it and then passed to ufits taxonomy to create a BIOM output file containing all metadata, OTUs, and taxonomy
• BIOM output of ufits taxonomy is compatible with QIIME, PHINCH, MetaCoMET, PhyloSeq, etc.
• ufits filter now alerts user if passing a barcode name via -b is not found in OTU table

ufits v0.5.6

• updated UFITS with better logging for external programs, so now log file should be more informative if you run into any errors. this will help me diagnose the problem.
• bug fix for ufits dada2 where script would die if --uchime_ref option not passed

ufits v0.5.5

• update to COI database. Previous version had some mistakes in re-formating the BOLD database. Scripts and workflow on how this database was constructed is available here
• updates to ufits dada2 pipeline. Script will now also create bOTUs (biological OTUs) as the DADA2 output is sensitive to 1 bp, thus a single "species" may be spread out over several iSeqs. Therefore, to accommodate downstream community ecology statistics, these iSeqs are clustered at a set threshold (-p, --pct_otu) to collapse "species" into OTUs.
• updates to ufits data2 so that it builds an OTU table in same manner as ufits cluster, i.e. original reads are mapped to iSeqs (as opposed to DADA2 only using quality filtered data for OTU table generation).

ufits v0.5.4

• added support for reference chimera filtering in the ufits dada2 OTU picking method

ufits v0.5.3

• improve the terminal output of ufits dada2 as well as the Rscript logging

ufits v0.5.2

• 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

ufits v0.5.1

• 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.