2023.5.0

What's Changed

• ENH: @misialq added a new action for fetching whole genomes and taxonomies from NCBI databases, get-ncbi-genomes! 🥳
• ENH: @mikerobeson added a new action for getting sequence and taxonomy data from GTDB, get-gtdb-data! 🎉
• MAINT: @mirand863 updated orient-seqs to use VSEARCH orient under the hood for higher efficiency. This has resulted in deprecation of some parameters that are not compatible with orient.

Full Changelog: 2023.2.0...2023.5.0

2023.2.0

What's Changed

• DEP: Fix joblib for ncbi.py by @mikerobeson in #147
• MAINT: Add future deprecation warning for orient-seqs by @mirand863 in #150
• ENH: enables merge-taxa and dereplicate to handle user-defined rank handles. by @mikerobeson in #133
• ENH: initial draft of get-gtdb by @mikerobeson in #154

New Contributors

• @mirand863 made their first contribution in #150

Full Changelog: 2022.8.0...2023.2.0

2022.8.0

What's Changed

• Adds reverse complementing to orient-seqs by @jwdebelius in #121
• drop experimental loo cv method by @nbokulich in #130
• update readme by @nbokulich in #132
• dep: update pinnings by @thermokarst in #137
• dep/bug: missing vsearch dependency by @thermokarst in #139
• Adds Manuscript DOI badge to README by @mikerobeson in #141
• ENH: add vsearch's --qsegout option to extract reads by @mikerobeson in #140
• pin joblib to version 1.1 by @nbokulich in #144
• update readme for q2-2022.8 by @mikerobeson in #142
• MAINT: update copyright headers by @misialq in #148

New Contributors

• @jwdebelius made their first contribution in #121

Full Changelog: 2021.11.0...2022.8.0

2021.11.0

• MAINT: update rescript citation to PLoS Comp Bio by @mikerobeson in #120

2021.8.0

• ENH: added LSU-138 to get-silva-data by @mikerobeson in #99
• MAINT: issue-98 : updated minimum qiime 2 version in docs by @mikerobeson in #100
• MAINT: removal of RESCRIPt RNA types, etc.. by @mikerobeson in #102
• ENH: add support for fetching protein seqs from NCBI by @misialq in #92
• MAINT: A couple of tweaks for get-ncbi-data by @BenKaehler in #101
• MAINT: add visualization gallery link by @misialq in #110
• BUG: set unresolved taxonomies to 'Unassigned' by @misialq in #114
• BUG: fix 'Taxon' column to always be first after merge by @misialq in #113
• ENH: reverse transcribe support for aligned RNA fasta by @nbokulich in #115
• ENH: replace-taxonomy action by @mikerobeson in #116
• CI: alpha library api tweaks by @thermokarst in #118

2021.8.0.dev0

RESCRIPt 2021.8.0.dev0

2021.4.0.dev0

RESCRIPt 2021.4.0.dev0

2021.2.0

MAINT: update feature-classifier default params (#95)
ENH: use add-fragments flag when aligning primers for trimming (#91)
IMP: add fasta subsampling action (#87)
IMP: add alignment trimming action (#85)

2020.11

• IMP: improvements to get-ncbi-data (make more robust to server-side errors, hangups)
• IMP: Support for SILVA 138.1
• IMP: parallelise sequence processing
• IMP: adds ability to NOT propagate SILVA taxonomy
• ENH: added filter-taxa method
• IMP: adds super to dereplicate
• IMP: additional evaluate CV options
• README: more tutorials, updates
• biorxiv preprint citation (README and plugin registration)

2020.6.1

• Adds get_ncbi_data to automatically acquire sequence/taxonomy data from genbank based on a user-defined query or list of accessions.

• various enhancements and bug fixes for dereplicate and evaluate-cross-validate