v1.3.1

New features

• Added sqm_mapper.pl, an utility script that maps reads to a given reference using Bowtie2 or BWA and provides estimation of the abundance of the contigs and ORFs in the reference.
• Added the make_databases_alt.pl, which works like make_databases.pl but tries to download the data from a different mirror.

Minor changes / bugfixes

• Fixed a bug in which the --cleaning would use clean reads for assembly, but all the reads for mapping.
• Added multithreading for parsing SAM results in Step 10.
• Removed RPKM columns from tables 19 and 20.
• test_install.pl now also checks the integrity of the nr.dmnd and taxid.db databases, making it easier to spot a corrupted database installation.
• Anvi`o v7 is now oficially supported.
• SQMtools: fixed a bug in which subsetting only one ORF would fail.
• SQMtools: fixed a bug that appeared in v1.3, in which Unmapped reads were incorrectly calculated when subsetting SQM objects.
• SQMtools: fixed a bug in which ORF TPMs were not properly rescaled after using rescale=T in any of the subset functions.
• SQMtools: we now use contig taxonomies for the nofilter and prokfilter modes, instead of ORF taxonomies. This gets rid of a bug that appeared in v1.3, in which reads mapping to contigs but not ORFs were incorrectly treated as Unmapped.

Compatibility Changes

• loadSQM (from SQMtools) and sqm2tables.py will fail when trying to parse projects created with versions prior to v1.3.1. To make the project work in 1.3.1, please:
  1. Run step 9 again (perl 09.summarycontigs3.pl /path/to/your/project).
  2. Remove the /path/to/your/project/results/tables, if present.

As always, please open an issue if something's not working for you.