thapbi-pict

Released on PyPI on 2021-03-30:

https://pypi.org/project/thapbi-pict/0.7.11/

The thapbi_pict assess command was simplified to only operate at sample/species level.

The thapbi_pict classify command now has an optional minimum abundance argument, useful when you have been exploring lower abundance thresholds but wish to run a slower classifier only on the more abundant sequences.

Some documentation updates too, reflecting recent changes.

Released on PyPI on 2021-03-24:

https://pypi.org/project/thapbi-pict/0.7.10/

The pipeline command now includes calling the fasta-nr command, making non-redundant FASTA file of all the sequences being analysed.

Released on PyPI on 2021-03-15:

https://pypi.org/project/thapbi-pict/0.7.9/

Option to show unsequenced entries in summary sample report (-u or --unsequenced).

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.

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.

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.

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.

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.

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+.

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.

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.

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.

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.

This is a belated release on GitHub, with v0.5.8 published on PyPI 2019-12-13

https://pypi.org/project/thapbi-pict/0.5.8/

The v0.5.x series focussed on the use of HMMs, which are now only used to describe control sequences. Specifically, a marker specific HMM is not longer used, making the tool easier to apply to other marker sequences.

This is a belated release on GitHub, with v0.4.19 published on PyPI 2019-11-19

https://pypi.org/project/thapbi-pict/0.4.19/

The v0.4.x series focussed on the curated Phytophthora ITS1 database, including adding NCBI taxonomy synonym support.

The read preparation step now applies the control based minimum abundance threshold at folder level (each 96-well plate or other batch should be in a separate folder).