THAPBI PICT v0.7.8

Released on PyPI on 2021-03-11:

https://pypi.org/project/thapbi-pict/0.7.8/

Fixed Nothophytophthora valdiviana entry in the default DB, added in the last release but with gap characters present.

Database importing now blocks gaps or anything other than IUPAC DNA letters.

THAPBI PICT v0.7.7

Released on PyPI on 2021-02-24:

https://pypi.org/project/thapbi-pict/0.7.7/

This release focused on improving the coverage of the default Phytophthora centric ITS1 database. It added 12 novel species from Català et al. (2018), hand curated Nothophytophthora sequences, additional single isolate controls, and expanded the NCBI import of published sequences (at genus level only) to include all Oomycota and refined this to avoid importing partial sequences.

This work markedly reduced the number of unknown sequences in our tree nursery and environmental survey work.

THAPBI PICT v0.7.6

Released on PyPI on 2021-02-17:

https://pypi.org/project/thapbi-pict/0.7.6/

Replaced thapbi_pict seq-import command for adding single isolate FASTQ files to a DB, with thapbi_pict curated-seq for turning them into small FASTA files for use with thapbi_pict curated-import. This allows us to keep our single isolates sequenced July 2018 under version control, for use when building default DB.

There is no change to the sequences in the provided default database with this release.

THAPBI PICT v0.7.5

Released on PyPI on 2021-02-16:

https://pypi.org/project/thapbi-pict/0.7.5/

Refined the default DB by adjusting how the genus-level NCBI import is trimmed. There are now less entries in the provided database, but we have removed poorly trimmed entries which would be useless with most of the classifier methods.

THAPBI PICT v0.7.4

Released on PyPI on 2021-02-15:

https://pypi.org/project/thapbi-pict/0.7.4/

Edit-graph now include genus-only labels.

New 1s2g, 1s4g & 1s5g classifiers - like the recently added 1s3g but with different edit-distance thresholds for assigning a genus level match.

v0.7.3 - Updated NCBI import & taxonomy. New 1s3g classifier. Use cutadapt v3.0+.

This is a belated release on GitHub, with v0.7.3 published on PyPI 2021-01-29

https://pypi.org/project/thapbi-pict/0.7.3/

Updated NCBI import & taxonomy. New 1s3g classifier. Use cutadapt v3.0+.

v0.7.2 - Added command for use with interactive ENA read submission.

This is a belated release on GitHub, with v0.7.2 published on PyPI 2020-10-06

https://pypi.org/project/thapbi-pict/0.7.2/

Added --ena-submit command for use with interactive ENA read submission.

v0.7.1 - Curated Phytophthora DB minor updates. Classifier output in edit-graph.

This is a belated release on GitHub, with v0.7.1 published on PyPI 2020-09-29

https://pypi.org/project/thapbi-pict/0.7.1/

Curated Phytophthora DB minor updates. Classifier output in edit-graph.

v0.7.0 - Reports now include FASTQ statistics

This is a belated release on GitHub, with v0.7.0 published on PyPI 2020-04-02

https://pypi.org/project/thapbi-pict/0.7.0/

Read counts etc now stored as a header in intermediate FASTA files, and shown in reports.

Final release from the v0.6.x series

This is a belated release on GitHub, with v0.6.15 published on PyPI 2020-03-12

https://pypi.org/project/thapbi-pict/0.6.15/

The v0.6.x series focuses on improved reporting. Additionally, the marker sequences in the default curated Phytophthora ITS1 database were extended to include the leading normally conserved 32bp region which had previously been discarded.