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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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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
Record which samples are controls
#534
peterjc
closed
1 year ago
0
Apply min_abundance in parse_sample_tsv
#533
peterjc
closed
1 year ago
0
[pre-commit.ci] autoupdate
#532
pre-commit-ci[bot]
closed
1 year ago
0
Record control status in sample-tally outputs
#531
peterjc
closed
1 year ago
0
Apply minimum total abundance in sample-tally
#530
peterjc
closed
1 year ago
0
Use sample-tally TSV in place of FASTA inputs to edit-graph
#529
peterjc
closed
1 year ago
0
Use samples-tally TSV in the assess command
#528
peterjc
closed
1 year ago
0
Abundance thresholding in sample-tally
#527
peterjc
closed
1 year ago
1
Use 'python -m build' to make tar-ball and wheel
#526
peterjc
closed
1 year ago
0
Update to Oct 2022 NCBI taxonomy; no DB changes
#525
peterjc
closed
1 year ago
0
Supplement <stem>.all_reads.fasta with <stem>.tally.tsv
#524
peterjc
closed
1 year ago
1
[pre-commit.ci] autoupdate
#523
pre-commit-ci[bot]
closed
1 year ago
0
Refactor to centralise writing classifier output
#522
peterjc
closed
1 year ago
0
Always replace classifier output
#521
peterjc
closed
1 year ago
0
BIOM table export
#520
peterjc
closed
1 year ago
4
assess command slow with large DB
#519
peterjc
opened
1 year ago
0
Update to Oct 2022 NCBI taxonomy; no DB changes
#518
peterjc
closed
1 year ago
0
Segmentation fault from rapidfuzz-2.11.0
#517
peterjc
closed
2 years ago
2
[pre-commit.ci] autoupdate
#516
pre-commit-ci[bot]
closed
2 years ago
2
Pest insects worked example, Batovska et al. (2021)
#515
peterjc
closed
1 year ago
6
How to handle species without a genus?
#514
peterjc
opened
2 years ago
2
Speedup substr classifier
#513
peterjc
closed
2 years ago
1
Use more bulk DB importing
#512
peterjc
closed
2 years ago
3
Update to NCBI results from 2022-09-16
#511
peterjc
closed
2 years ago
0
Cap tools by available CPUs
#510
peterjc
closed
2 years ago
0
Accept .fq or .fq.gz in addition to .fastq(.gz)
#509
peterjc
closed
2 years ago
0
Bulk import with SQLalchemy
#508
peterjc
closed
2 years ago
3
DB import scales poorly with large datasets
#507
peterjc
closed
2 years ago
6
Use single RapidFuzz cdist call instead of variant clouds
#506
peterjc
closed
2 years ago
4
Use RapidFuzz cdist instead of Levenshtein distance in inner loop
#505
peterjc
closed
2 years ago
1
[pre-commit.ci] autoupdate
#504
pre-commit-ci[bot]
closed
2 years ago
2
Clarify incremental updates to Oomycota_ITS1_obs.fasta
#503
peterjc
closed
5 months ago
1
Add new curated Phytophthora entries from Jung et al 2022
#502
peterjc
closed
2 years ago
1
Update NCBI search as of 2022-08-17
#501
peterjc
closed
2 years ago
0
Add new curated Phytophthora entries from Jung et al 2022
#500
peterjc
closed
2 years ago
2
Insert missing T or TT from start of NCBI seqs; stricter 32bp check
#499
peterjc
closed
2 years ago
1
Require 31bp overlap with 32bp leader
#498
peterjc
closed
2 years ago
1
Improving left trimming in yyyy-mm-dd_ITS1_Oomycota_w32.fasta
#497
peterjc
closed
2 years ago
5
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