Browsing by Autor "bioRoastery"

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    gbouras13/pharokka: v1.8.2
    (European Organization for Nuclear Research, 2025) George Bouras; Lander De Coninck; Alistair Legione; Camilo García; Martin Larralde; bioRoastery; George Chlipala; Hugo Ávila; Joon Klaps; Paul Mennig
    Integration with suvtk to make to it easier to submit Pharokka and Phold annotated genomes to Genbank - thanks to @LanderDC for suvtk and integration. See https://github.com/gbouras13/pharokka?tab=readme-ov-file#genbank-submission for more details Various small bug fixes
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    gbouras13/pharokka: v1.9.0
    (European Organization for Nuclear Research, 2026) George Bouras; Lander De Coninck; Alistair R. Legione; Camilo García; Martin Larralde; bioRoastery; George E. Chlipala; Hugo Ávila; Joon Klaps; Paul Mennig
    Adds pyrodigal-rv (see https://github.com/LanderDC/pyrodigal-rv) dependency as a gene predictor option that may be useful if you are annotating RNA phages (also RNA viruses generally perhaps, although YMMV) Use -g pyrodigal-rv to use this Fixes bug with incorrect translation table being passed when using -g prodigal and meta mode (usually for single phages, where they are too small to have a Prodigal model trained for them) - see #409 We recommend you use -g prodigal-gv (the default) if you have metagenomic datasets anyway Adds --reverse_mmseqs2 flag - this makes the PHROG MMseqs2 profile database the target not the query (thanks @simroux). This in only recommended for enormous datasets. Adds --sensitivity as a CLI option - controls MMseqs2 profile search sensitivity
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    gbouras13/pharokka: v1.9.1
    (European Organization for Nuclear Research, 2026) George Bouras; Lander De Coninck; Alistair Legione; Camilo García; Martin Larralde; bioRoastery; George E. Chlipala; Hugo Ávila; Joon Klaps; Paul Mennig
    Updates [pyhmmer](https://github.com/althonos/pyhmmer] dependency to v0.12.0 - thanks @althonos for the above and beyond support Fixes various Python 3.13 pandas v2 bugs