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peterjc
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thapbi-pict
Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
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Remove 'Phytophthora austrocedri' workaround
#584
peterjc
closed
5 months ago
1
Type annotations in main code
#583
peterjc
closed
4 months ago
1
[pre-commit.ci] autoupdate
#582
pre-commit-ci[bot]
closed
6 months ago
0
[pre-commit.ci] autoupdate
#581
pre-commit-ci[bot]
closed
7 months ago
0
Automate NCBI updates with esearch and efetch
#580
peterjc
closed
7 months ago
0
Record the full length synthetic controls incuding primers
#579
peterjc
closed
7 months ago
0
[pre-commit.ci] autoupdate
#578
pre-commit-ci[bot]
closed
8 months ago
1
Drop unused -m / --method from edit-graph; version bump to 1.0.4
#577
peterjc
closed
8 months ago
0
Assorted minor fixes from the ruff linter
#576
peterjc
closed
8 months ago
0
Replace black with ruff format command
#575
peterjc
closed
8 months ago
1
[pre-commit.ci] autoupdate
#574
pre-commit-ci[bot]
closed
9 months ago
0
Adding two P. condilina sequences to the curated DB
#573
peterjc
closed
10 months ago
0
Update NCBI entries in default DB
#572
peterjc
closed
10 months ago
1
Update to August 2023 NCBI taxonomy
#571
peterjc
closed
10 months ago
0
Add mypy configuration for basic type checking
#570
peterjc
closed
6 months ago
2
[pre-commit.ci] autoupdate
#569
pre-commit-ci[bot]
closed
11 months ago
0
Enhancements to the plot_reduction.py script
#568
peterjc
closed
10 months ago
1
Worked example change from v1.0.0 to v1.0.1
#567
peterjc
closed
11 months ago
0
Preserve cutadapt, singletons, etc in pooled reports
#566
peterjc
closed
11 months ago
1
Pooled marker counts for cutadapt, singletons for scripts/plot_reduction.py
#565
peterjc
closed
11 months ago
0
Sample tally tweaks
#564
peterjc
closed
11 months ago
1
chimera regression with VSEARCH 2.23.0
#563
peterjc
closed
11 months ago
1
[pre-commit.ci] autoupdate
#562
pre-commit-ci[bot]
closed
1 year ago
0
[pre-commit.ci] autoupdate
#561
pre-commit-ci[bot]
closed
1 year ago
0
Bump minimum Python to 3.7
#560
peterjc
closed
1 year ago
0
Script to create read data reduction stacked line plot
#559
peterjc
closed
1 year ago
0
Allow singletons in pipeline
#558
peterjc
closed
1 year ago
0
[pre-commit.ci] autoupdate
#557
pre-commit-ci[bot]
closed
1 year ago
0
Enhancement: Configurable colour mapping for edit-graph
#556
peterjc
opened
1 year ago
0
[pre-commit.ci] autoupdate
#555
pre-commit-ci[bot]
closed
1 year ago
0
Use biom export-metadata to check test output
#554
peterjc
closed
4 months ago
3
Make BIOM output optional via --biom flag
#553
peterjc
closed
1 year ago
0
BIOM export of the read report
#552
peterjc
closed
1 year ago
0
BIOM output from classifier
#551
peterjc
closed
1 year ago
3
Update assess command to work on sample-tally with classificatoin
#550
peterjc
closed
1 year ago
0
Append classifier columns to sample-tally TSV
#549
peterjc
closed
1 year ago
3
Record any chimera status in sample-tally final column
#548
peterjc
closed
1 year ago
1
Restore FASTA input for edit-graph?
#547
peterjc
opened
1 year ago
0
Note chimeras if denoising with USEARCH or VSEARCH
#546
peterjc
closed
1 year ago
0
[pre-commit.ci] autoupdate
#545
pre-commit-ci[bot]
closed
1 year ago
0
Use 'unoise-l' to be explict about Levenshtein distance UNOISE
#544
peterjc
closed
1 year ago
0
Wrap vsearch and usearch for UNOISE read-correction
#543
peterjc
closed
1 year ago
2
Finish UNOISE distance-based greedy clustering (DGC)
#542
peterjc
closed
1 year ago
0
Add UNOISE alpha and gamma to command line
#541
peterjc
closed
1 year ago
3
Assess soil nematodes
#540
peterjc
closed
1 year ago
0
Discussion for soil_nematodes example
#539
peterjc
closed
1 year ago
2
UNOISE within sample-tally step
#538
peterjc
closed
1 year ago
6
[pre-commit.ci] autoupdate
#537
pre-commit-ci[bot]
closed
1 year ago
0
Ignore controls not part of the input argument
#536
peterjc
closed
1 year ago
1
Only apply abundance threshold in sample-tally
#535
peterjc
closed
1 year ago
2
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