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Recent Releases of https://github.com/biodiversitydata-se/coidb

https://github.com/biodiversitydata-se/coidb - Version 0.5.2

What's Changed

  • Update default links by @johnne in https://github.com/biodiversitydata-se/coidb/pull/24

Full Changelog: https://github.com/biodiversitydata-se/coidb/compare/v0.5.1...v0.5.2

- Python
Published by johnne about 2 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.5.1

What's Changed

  • Add possibility to generate subsequences of references matching amplicon region (EXPERIMENTAL)
  • Update links to GBIF release in default config
  • Update BOLD bin column used in latest GBIF release
  • Add touch Snakemake option

Full Changelog: https://github.com/biodiversitydata-se/coidb/compare/v0.4.8...v0.5.1

- Python
Published by johnne about 2 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.4.8

  • Set default identity threshold to 1.0
  • Add script to format output for sintax

- Python
Published by johnne over 3 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.4.7

  • Increase threads in clustering rule
  • Remove reference to cluster.yml file in clustering rule

- Python
Published by johnne almost 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.4.6

Update non-uniqueness strategy

What's Changed

  • Devel by @johnne in https://github.com/johnne/coidb/pull/17

Full Changelog: https://github.com/johnne/coidb/compare/v0.4.5...v0.4.6

- Python
Published by johnne about 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.4.5

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.4.3

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.4.1

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.4.0

Merge devel branch

Changelog:

  • Change to using setup.cfg
  • Make use of GBIF backbone taxonomy
  • Better handling of intermediate ranks
  • Trim sequences using seqkit(faster)

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.3.3

Changelog: - Add cleaning rule to strip vsearch specific strings from fasta

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.3.2

Changelog

  • Properly update sequences after trimming gaps and terminal N

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.3.1

Changelog - Translate characters to uppercase when filtering non-standard nucleotides

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.3.0

Changelog: - Include filtering of sequences with non-standard nucleotides. - Split download and extraction steps

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.2.4

Changelog:

  • Sort sequences by BOLD cluster id when clustering

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.2.3

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.2.1

Changelog: - Update string splitting when extracting species names for BOLD bins

- Python
Published by johnne over 4 years ago

https://github.com/biodiversitydata-se/coidb - Version 0.2

Changelog

  • Downloads an additional file from GBIF (ibol_bins_2021_02_08.zip) for mapping BOLD bin ids to species name

Minor fixes

  • Remove --show-failed-logs from snakemake call

- Python
Published by johnne almost 5 years ago

https://github.com/biodiversitydata-se/coidb - First pre-release

Working release pending more extensive testing

- Python
Published by johnne about 5 years ago