THAPBI PICT v1.0.20

Released on PyPI 2024-12-31:

https://pypi.org/project/thapbi-pict/1.0.20/

Script sample_filter.py now accepts multiple (classified) tally files. This can be used to pool multiple separate runs of the pipeline (e.g. one per plate).

Promoted MT065831.1 Phytophthora nicotianae in the default database to species level.

The helper scripts will now use rich-argparse if installed for more colorful command line help.

Fixed a scaling issue in the summary reports for large datasets.

Added SBATCH headers to the worked example run.sh scripts for use on a SLURM compute cluster.

Fixed some minor cross-platform and initial setup issues in the worked examples.

THAPBI PICT v1.0.19

Released on PyPI 2024-12-05:

https://pypi.org/project/thapbi-pict/1.0.19/

Updated curated entries and NCBI bulk genus-only import in the default Phytophthora focused ITS1 database.

THAPBI PICT v1.0.18

Released on PyPI 2024-11-25:

https://pypi.org/project/thapbi-pict/1.0.18/

The ena-submit command was updated for the current ENA expectations, 12 manadatory fields for uploading paired FASTQ files. This now requires the study accession, but no longer requires an insert size etc.

The default ITS1 DB was updated to use the November 2024 NCBI taxonomy, which now has a taxid for Phytophthora heteromorpha.

THAPBI PICT v1.0.17

Released on PyPI 2024-11-08:

https://pypi.org/project/thapbi-pict/1.0.17/

This is mostly a maintenance release bumping the minimum version to Python 3.10, and updating the versions of the dependencies to their current known working releases.

This also adds additional cosmetic functionality if the Python library rich-argpase is installed: The command line help parsing will now display in colour if your terminal supports this.

THAPBI PICT v1.0.16

Released on PyPI 2024-09-09:

https://pypi.org/project/thapbi-pict/1.0.16/

Drops empty rows/columns (all zero read counts) in the reports when using --requiremeta or -q to hide samples without metadata.

This release also updates the default ITS1 database slightly, adopting the September 2024 NCBI taxonomy and adding a few more reference sequences affecting non-Phytophthora only.

THAPBI PICT v1.0.15

Released on PyPI 2024-09-05:

https://pypi.org/project/thapbi-pict/1.0.15/

Updated the default ITS1 database with additional curated entries, many from Jung et al. (2024), and the NCBI taxonomy as of August 2024. See:

Jung et al. (2024) Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity https://doi.org/10.3114/sim.2024.107.04

This included renaming our placeholder Phytophthora taxon ad7988a to Phytophthora sp. taxon castitis as per KC478759:

Bertier et al. (2013) The expansion of Phytophthora clade 8b: three new species associated with winter grown vegetable crops https://doi.org/10.3767%2F003158513X668554

THAPBI PICT v1.0.14

Released on PyPI 2024-08-26:

https://pypi.org/project/thapbi-pict/1.0.14/

Added a fifth synthetic control to the default DB, now used in the revised protocol at the Hutton Institute to construct mock-communities with magnitude steps in concentration, for use with the Illumina NextSeq and potentially higher read depth.

The pipeline and prepare-reads commands now support an optional -k or --markers argument to restrict the analysis to a subset of the markers defined in a multiple-marker database. An example use-case would be processing our historic MiSeq plates using ITS1 only when using a DB containing ITS1 and rps10 marker definitions. The default remains looking for all defined markers.

THAPBI PICT v1.0.13

Released on PyPI 2024-05-22:

https://pypi.org/project/thapbi-pict/1.0.13/

Updated the default Phytophthora focused ITS1 database with a more recent NCBI search, taxonomy, etc.

Stops using freeze-panes in Excel output which was no longer practical with small screens and/or lots of metadata.

THAPBI PICT v1.0.12

Released on PyPI on 2024-03-11:

https://pypi.org/project/thapbi-pict/1.0.12/

Fixes the inadvertent use of type-annotation syntax which had required Python 3.9 or later since THAPBI PICT v1.0.9. This release is tested on and requires at least Python 3.8.

Graceful edit-graph failure if missing graphviz fdp command line tool.

Heuristics for importing sequences in SINTAX style when missing genus in the species field.

Metadata argument -x now accepts multiple columns.

THAPBI PICT v1.0.11

Released on PyPI on 2024-03-05:

https://pypi.org/project/thapbi-pict/1.0.11/

Harmonised the ASV naming used in the optional FASTA and BIOM output files to match the main TSV and Excel usage. The sample-tally command and stage of the pipeline can now optionally output a BIOM file.

Importing the (pre-classifier) BIOM file and matching FASTA file of ASV sequences into Qiime2 has been tested.