THAPBI PICT v0.11.6

Released on PyPI on 2022-03-09:

https://pypi.org/project/thapbi-pict/0.11.6/

Fixed a regression building summary reports when some samples have not been sequenced.

THAPBI PICT v0.11.5

Released on PyPI on 2022-02-18:

https://pypi.org/project/thapbi-pict/0.11.5/

Reporting enhancements when using spike-in (synthetic) controls.

THAPBI PICT v0.11.4

Released on PyPI on 2022-02-08:

https://pypi.org/project/thapbi-pict/0.11.4/

Updates the default DB with a further six Phytophthora species.

THAPBI PICT v0.11.3

Released on PyPI on 2022-02-01:

https://pypi.org/project/thapbi-pict/0.11.3/

Fixes the dynamic k-mer threshold for detecting synthetic spike-in control sequences.

THAPBI PICT v0.11.2

Released on PyPI on 2022-01-20:

https://pypi.org/project/thapbi-pict/0.11.2/

Small fixes for use on Windows, and automated continuous integration testing on Windows using AppVeyor.

THAPBI PICT v0.11.1

Released on PyPI on 2022-01-18:

https://pypi.org/project/thapbi-pict/0.11.1/

Switched from the python-Levenshtein to rapidfuzz Python library for Levenshtein edit-distance, which is more easily installed on Windows, and should be faster too.

THAPBI PICT v0.11.0

Released on PyPI on 2022-01-13:

https://pypi.org/project/thapbi-pict/0.11.0/

When used with multiple markers the pipeline now also produces combined reports by pooling the predictions from each marker.

THAPBI PICT v0.10.6

Released on PyPI on 2022-01-12:

https://pypi.org/project/thapbi-pict/0.10.6/

This fixes a slow-down in v0.10.0 when using a small database, most noticeable when exploring a large new dataset with a minimal (often ad-hoc) database. It restores the earlier approach of building a cloud of all 1bp edits of the DB entries in memory to speed up comparison to the samples sequences (as long as the DB is not too large as this becomes memory intensive).

THAPBI PICT v0.10.5

Released on PyPI on 2021-12-23:

https://pypi.org/project/thapbi-pict/0.10.5/

Default for -f / --abundance-fraction is now 0.001, meaning 0.1%. The percentage based abundance threshold was previously off by default.

THAPBI PICT v0.10.4

Released on PyPI on 2021-11-24:

https://pypi.org/project/thapbi-pict/0.10.4/

Updates to default curated DB, including newer NCBI taxonomy.