EUKulele - v2.1.2

• Fixed bugs in assigning maximum taxonomic levels to MAGs
• Made cutoffs for taxonomic levels more fully flexible

Scientific Software - Peer-reviewed - Python
Published by akrinos 8 months ago

EUKulele - v2.0.9

Update to prior release to add tab removal step for phylodb database. In this release, we address several long-standing issues in EUKulele and add a new feature.

• Changes the name of the pident column to reflect that it is really the best quality score
• Fixed issues related to errors of "MissingFromTaxDict" (https://github.com/AlexanderLabWHOI/EUKulele/issues/60)
• Allowed gzipped database fastas to be used (https://github.com/nf-core/metatdenovo/issues/256)
• Newest version of EukProt now downloads with EUKulele and EukProt protein map bugs have been resolved; gzipped version of fasta also downloads (https://github.com/AlexanderLabWHOI/EUKulele/issues/66)
• Fixed database download issues for GTDB add-on
• Updated calls to append with calls to concat (pandas)
• Fixed some instances of spaces being introduced to taxonomy strings during parsing

New feature: - Added a flag, --create_euk_fasta, to dump a fasta file of eukaryotic sequences after a EUKulele run (https://github.com/AlexanderLabWHOI/EUKulele/issues/35)

Scientific Software - Peer-reviewed - Python
Published by akrinos over 1 year ago

EUKulele - 2.0.9

In this release, we address several long-standing issues in EUKulele and add a new feature.

• Changes the name of the pident column to reflect that it is really the best quality score
• Fixed issues related to errors of "MissingFromTaxDict" (https://github.com/AlexanderLabWHOI/EUKulele/issues/60)
• Allowed gzipped database fastas to be used (https://github.com/nf-core/metatdenovo/issues/256)
• Newest version of EukProt now downloads with EUKulele and EukProt protein map bugs have been resolved; gzipped version of fasta also downloads (https://github.com/AlexanderLabWHOI/EUKulele/issues/66)
• Fixed database download issues for GTDB add-on
• Updated calls to append with calls to concat (pandas)
• Fixed some instances of spaces being introduced to taxonomy strings during parsing

New feature: - Added a flag, --create_euk_fasta, to dump a fasta file of eukaryotic sequences after a EUKulele run (https://github.com/AlexanderLabWHOI/EUKulele/issues/35)

Scientific Software - Peer-reviewed - Python
Published by akrinos over 1 year ago

EUKulele - v2.0.7

Updating README_db file, making changes to error reporting, sending draft release to bioconda to fix containerization issue

Scientific Software - Peer-reviewed - Python
Published by akrinos about 2 years ago

EUKulele - v2.0.6

In this release, we

• Updated URLs for use of GTDB as a reference database
• Revised code for use of --threads parameter within DIAMOND
• Changed dependencies

Scientific Software - Peer-reviewed - Python
Published by akrinos over 2 years ago

EUKulele - v2.0.5

Adding ability to use GTDB as database selection

Scientific Software - Peer-reviewed - Python
Published by akrinos almost 3 years ago

EUKulele - v2.0.3

• adding wget as a dependency

Scientific Software - Peer-reviewed - Python
Published by akrinos over 3 years ago

EUKulele - v2.0.2

Very small update to v2.0.1 for integration purposes.

Changed: - added quotes to URLs in wget calls to deal with wget utility type

Scientific Software - Peer-reviewed - Python
Published by akrinos over 3 years ago

EUKulele - v2.0.1

Added: - flag --consensus_proportion for setting LCA strictness. Defaults to 1 (identical bitscores will trigger LCA). A value of e.g. 0.95 would mean that bitscores within 95% of the max bitscore would be considered identical for the purposes of triggering LCA - flag --no_busco forces that BUSCO will not be run - BUSCO is no longer a dependency for installing EUKulele

Changed: - default for metaT file extension to .fasta instead of .fna

Scientific Software - Peer-reviewed - Python
Published by akrinos almost 4 years ago

EUKulele - v1.0.6

v1.0.6 catches bioconda up to latest EUKulele version available on PyPI. The major change involved in this update is making EUKulele use bitscore as default when selecting best matches, rather than relying on percentage identity as is used later in the taxonomic assignment process.

Scientific Software - Peer-reviewed - Python
Published by akrinos over 4 years ago

EUKulele - v1.0.4

Version 1.0.4 is to catch EUKulele up on bioconda to the latest version on PyPI. The main feature of this version is a fix to the taxonomy cutoffs YAML file which was needed following the change to the default database for EUKulele.

Scientific Software - Peer-reviewed - Python
Published by akrinos almost 5 years ago

EUKulele - v1.0.2b

First GitHub release of EUKulele, modified for Zenodo. Features new default MMETSP-MarRef database, and debuts the tool as a solution for taxonomic annotation of microbial eukaryotes.

Scientific Software - Peer-reviewed - Python
Published by akrinos almost 5 years ago

EUKulele - v1.0.2

First GitHub release of EUKulele. Features new default MMETSP-MarRef database, and debuts the tool as a solution for taxonomic annotation of microbial eukaryotes.

Scientific Software - Peer-reviewed - Python
Published by akrinos almost 5 years ago