MetaWorks v1.6.0

Added a new workflow to handle dual-indexed samples from individuals (as opposed to bulk samples).

MetaWorks v1.5.1

Corrected the raw.stats output file. Removed fasta.tmp files.

MetaWorks v1.5.0

Added a dataflow to process R1 and R2 files separately.

MetaWorks v1.4.1

Fixed a bug in snakemake_OTU so that you can properly use the latest custom-trained UNITE ITS reference database for ITS taxonomic assignments instead of the default reference database with the RDP Classifier.

MetaWorks v1.4.0

Added two additional dataflows to supplement the default ESV pipeline: a new OTU pipeline and a GLOBAL ESV pipeline.

MetaWorks v1.3.4

Replaced the Perl scripts add_seqs_to_tax.plx and add_seqs_to_tax2.plx with add_seqs_to_tax3.plx that now handles fasta files with line breaks in the sequence. In the final results.csv file, the full sequence is now shown instead of just the first line.

MetaWorks v1.3.3

Updated to use the conda version of the RDP Classifier v2.13 .
Updated to support the analysis of plant ITS taxonomic assignments using the PLANiTS reference set (Banchi et al., 2020). The RDP classifier trained plant ITS reference set is available from https://github.com/terrimporter/PLANiTS_ITSClassifier .

MetaWorks v1.3.2

Updated underlying programs:
VSEARCH is now v2.15.2
RDP Classifier is now v2.13
CUTADAPT is now v3.2
SNAKEMAKE is now 5.32

I now recommend that if MetaWorks is used to classify fungal ITS sequences, do not use the default fungalits_unite reference set from 2014, instead use the newer UNITE ITS Classifier from https://github.com/terrimporter/UNITE_ITSClassifier that is based on the UNITE v8.2 reference set (02-20-2020). The Perl script add_abundance_to_rdp_out8.plx was slightly modified to change the 'Domain' column header to 'Kingdom' to reflect the taxon names used in this custom trained UNITE reference set.

MetaWorks v1.3.1

For pseudogene removal method 1, the final file now only contains the taxa in the grep pattern (ex. Arthropoda) with an ORF sequence.

MetaWorks v1.3.0

Added two new parameters than can be adjusted for SeqPrep read pairing:
Maximum fraction of mismatches allowed in overlap and
Minimum fraction of matching overlap