Official version 1.0. Released on 9 February 2017.
Features
* Updated documentation to improve clarity on examples, file inputs and file outputs.
* Delete tmp files and split directory in deblur output directory
Backward-incompatible changes [stable]
* Removed the --skip-trimming flag and use --trim-length=-1 instead
* The trim length parameter is now required.
* Negative mode is always run. What that means is that an output is always generated with reads matching the negative database removed (an unfiltered output is still generated). By default, this means that any read which appears to be PhiX or Adapter will be filtered out.
* Change output file names to all.biom, all.seqs.fa, reference-non-hit.biom, reference-non-hit.seqs.fa, reference-hit.biom, reference-hit.seqs.fa. The term "reference" in this case refers to sequences which recruited (hit) to the positive database or failed to recruit (non-hit). Recruitment is performed using SortMeRNA and a sequence is retained if it aligns with an e-value of 10 or less (i.e., a coarse filter).
* Changed --min-reads default value to 10 (was 0) in accordance with the manuscript.
* Renamed --threads shortcut to -a (was -t) in remove_artifacts CLI
Performance enhancements
Bug fixes