optimotu_targets 4.1.1

optimotu_targets 4.1.0

Detection of spike sequences is now optional, and an option is also included for positive control sequences. Both of these options are under controls: in the configuration file. If either type of sequences should be detected, the file containing sequences to detect should be given as controls: spikes: or controls: positive: respectively. Note this is a breaking change for projects that did in fact use the default synmock spikes. These are included in protaxFungi as protaxFungi/amptk_synmock.fasta, but must now be explicitly specified.

Improved parsing of BOLD release datasets when used as outgroup references. It is now possible to directly download the BOLD_Public.DD-Mmm-YYYY.fasta.gz to supply as the file for outgroup_reference:sequences:. No separate taxonomy file is required. Note that execution will be a bit faster if the FASTA file is pre-filtered to include only sequences with "COI-5P" in the header, but this is not crucial, since this is more than 80% of the sequences in recent BOLD snapshots.

Initial public release, as described in arXiv preprint.