kalamari - Provenance

Added a ton of things but especially provenance. Why each genome was added.

- Perl
Published by lskatz over 1 year ago

kalamari - v5.7.2

Fixed a bug in downloadKalamari.sh

- Perl
Published by lskatz over 1 year ago

kalamari - v5.7.1

(no code changes)

• bumped the version to trigger a zenodo DOI

- Perl
Published by lskatz over 1 year ago

kalamari - v5.7.0

- Perl
Published by lskatz about 2 years ago

kalamari - v5.6.0

- Perl
Published by lskatz about 2 years ago

kalamari - v5.4.1

What's Changed

• More proper build by @lskatz in https://github.com/lskatz/Kalamari/pull/42

Full Changelog: https://github.com/lskatz/Kalamari/compare/v5.4.0...v5.5.0

• Scripts to build Kraken1, Kraken2
• Better unit tests
• Script to build taxonomy from diff
• Remove files outside of git versioning

- Perl
Published by lskatz about 2 years ago

kalamari - v5.4.0

Make things slightly more compatible with bioconda like setting the version in the executable

- Perl
Published by lskatz about 2 years ago

kalamari - v5.3.3

Making this release to coincide with the conda release

- Perl
Published by lskatz about 2 years ago

kalamari - v5.3.1

- Perl
Published by lskatz about 2 years ago

kalamari - v5.2.1

some minor CI changes and now --help gives exit code 0

- Perl
Published by lskatz over 3 years ago

kalamari - v5.2

• validate taxonomy script updated
• Better documentation
  • main doc
  • MIDAS database
• Fixed Salmonella subspecies IV and VIII

- Perl
Published by lskatz about 4 years ago

kalamari - v5.1

Fixed a bug where the same fasta entry would be downloaded and given its own taxid and also its parent taxid. Same fasta entry, duplicated, different headers.

- Perl
Published by lskatz almost 5 years ago

kalamari - v5.0

Merged mobsuite amazingness and cleaned up src folder considerably

- Perl
Published by lskatz almost 5 years ago

kalamari - v3.9.3

• Minimalistic taxonomy file
• parent IDs in tsv files
• fixed Escherichia albertii

- Perl
Published by lskatz almost 5 years ago

kalamari - v4.0

Finally a release with both chromosomes and plasmids in their own files and with good taxonomy.

• some species still missing :(

- Perl
Published by lskatz almost 6 years ago

kalamari - v3.9

• Releases now include taxonomy files. Taxonomy files are minimized versions that only include relevant taxa. NCBI taxonomy files have gone from >100M to >100K.
• Now includes Giardia and Cryptosporidium, and our first virus SARS-COV-2

- Perl
Published by lskatz about 6 years ago

kalamari - Version 3.5 with missing accessions

Several genomes are not online still and therefore do not have accessions.

• Download script available
• Instructions for how to install for Kraken and Kraken2
• Test script for installing with Kraken2

- Perl
Published by lskatz about 7 years ago