Release History
Version |
Date |
Notes |
|---|---|---|
v1.0.12 |
2024-03-11 |
Restored Python 3.8 support. More robust import of SINTAX style FASTA files. |
v1.0.11 |
2024-03-05 |
Harmonize ASV naming in BIOM output, optional |
v1.0.10 |
2024-02-26 |
Sample report ‘Unique’ column is now the unique ASV count. Misc updates. |
v1.0.9 |
2024-02-12 |
Using Python type annotations (internal code change). Python 3.9 onwards. |
v1.0.8 |
2024-02-06 |
Additional curated Phytophthora in default DB. Adds |
v1.0.7 |
2024-01-29 |
Treat Phytophthora cambivora as a synonym of Phytophthora x cambivora. |
v1.0.6 |
2024-01-24 |
Added some Peronosclerospora to curated DB. Updated NCBI import. |
v1.0.5 |
2023-11-22 |
Updated NCBI import, and scripted most of what was a semi-manual process. |
v1.0.4 |
2023-11-20 |
Dropped unused |
v1.0.3 |
2023-09-04 |
Updated NCBI import and curated P. condilina entries in default DB. |
v1.0.2 |
2023-08-18 |
Use sum of cutadapt and singleton values etc for pooled marker reports. |
v1.0.1 |
2023-07-26 |
Fixed some rare corner-case read-corrections in |
v1.0.0 |
2023-05-19 |
Minor documentation changes, linked to Cock et al. (2023) preprint. |
v0.14.1 |
2023-03-13 |
Optional BIOM output using the |
v0.14.0 |
2023-03-02 |
Offers UNOISE read-correction, built-in or invoking USEARCH or VSEARCH. |
v0.13.6 |
2022-12-28 |
Factional abundance threshold in |
v0.13.5 |
2022-12-21 |
Misc small fixes and documentation updates. |
v0.13.4 |
2022-12-07 |
Support abundance thresholding in the |
v0.13.3 |
2022-11-25 |
Using new |
v0.13.2 |
2022-11-11 |
Sped up |
v0.13.1 |
2022-09-21 |
Minor default DB update. Cap |
v0.13.0 |
2022-09-14 |
Sped up distance based classifiers by better use of RapidFuzz library. |
v0.12.9 |
2022-08-19 |
Updates default DB with new curated species and improved left trimming. |
v0.12.8 |
2022-08-08 |
Treat NCBI taxonomy ‘equivalent name’ as a synonym. Minor DB update. |
v0.12.7 |
2022-07-26 |
NCBI taxid in genus-only fallback classifier output. Minor DB update. |
v0.12.6 |
2022-07-25 |
Changes to how NCBI sequences are trimmed for use in the default DB. |
v0.12.5 |
2022-07-08 |
Merged/child NCBI taxid entries as synonyms. Import FASTA with taxid. |
v0.12.4 |
2022-07-07 |
Updated edit-graph code to work with RapidFuzz v2.0.0 or later. |
v0.12.3 |
2022-07-06 |
Updated NCBI taxonomy and bulk genus-only entries in default DB. |
v0.12.2 |
2022-06-15 |
Updates to the curated entries in the default Phytophthora ITS1 DB. |
v0.12.1 |
2022-05-18 |
Fix missing field regression on reports including unsequenced samples. |
v0.12.0 |
2022-04-19 |
Set fractional abundance threshold via synthetic spike-ins. Cutadapt v4.0+. |
v0.11.6 |
2022-03-09 |
Fix regression on reports including unsequenced samples. |
v0.11.5 |
2022-02-18 |
Reporting enhancements when using spike-in (synthetic) controls. |
v0.11.4 |
2022-02-08 |
Updates to default curated DB, adding several more Phytophthora species. |
v0.11.3 |
2022-02-01 |
Fix dynamic k-mer threshold for synthetic spike-in control sequences. |
v0.11.2 |
2022-01-20 |
Windows testing on AppVeyor, with minor Windows specific fixes. |
v0.11.1 |
2022-01-18 |
Using |
v0.11.0 |
2022-01-13 |
Multi-marker reports, pooling predictions from each marker. |
v0.10.6 |
2022-01-12 |
Fixed slow-down in v0.10.0 on large datasets with small DB. |
v0.10.5 |
2021-12-23 |
Default for |
v0.10.4 |
2021-11-24 |
Updates to default curated DB, including newer NCBI taxonomy. |
v0.10.3 |
2021-11-19 |
New |
v0.10.2 |
2021-11-05 |
Updates to default curated DB. Small changes to NCBI taxonomy loading. |
v0.10.1 |
2021-07-28 |
Fix for using SQLAlchemy v1.3 (previous release needed v1.4). |
v0.10.0 |
2021-07-28 |
Rework to handle larger DB and multiple markers. Modifies DB schema. |
v0.9.9 |
2021-07-08 |
Drop SWARM based classifiers. Single intermediate TSV file in pipeline. |
v0.9.8 |
2021-06-17 |
Drop edit-graph in pipeline. Require full length primers in merged reads. |
v0.9.7 |
2021-06-04 |
USEARCH SINTAX & OBITools FASTA conventions in |
v0.9.6 |
2021-05-21 |
Update default DB taxonomy, Peronosporales & Pythiales max 450bp. |
v0.9.5 |
2021-05-10 |
Simplify to just one |
v0.9.4 |
2021-05-05 |
Drop unused metadata fields in DB schema. Fix GML format edit graphs. |
v0.9.3 |
2021-05-04 |
Drop HMM for spike-in control detection, now via DB & k-mer counting. |
v0.9.2 |
2021-04-28 |
Fix obscure problem using relative versions of absolute paths. |
v0.9.1 |
2021-04-20 |
Set metadata encoding. Spike-in HMM default now off. |
v0.9.0 |
2021-04-19 |
Drop use of Trimmomatic, faster and slightly higher read counts. |
v0.8.4 |
2021-04-13 |
Sped up re-running by delaying method setup until and if required. |
v0.8.3 |
2021-04-13 |
Include abundance threshold in summary reports (if varied by sample). |
v0.8.2 |
2021-04-13 |
Sample report pooling script. Fix |
v0.8.1 |
2021-04-09 |
Drop species list embedded in intermediate TSV, |
v0.8.0 |
2021-04-06 |
Revise genus/species columns in sample report. Add |
v0.7.11 |
2021-03-30 |
|
v0.7.10 |
2021-03-24 |
Pipeline includes |
v0.7.9 |
2021-03-15 |
Option to show unsequenced entries in summary sample report ( |
v0.7.8 |
2021-03-11 |
Only import IUPAC DNA characters to DB. Fix N. valdiviana in default DB. |
v0.7.7 |
2021-02-24 |
Revise default ITS1 DB: NCBI Oomycetes, more curation & single isolates. |
v0.7.6 |
2021-02-17 |
|
v0.7.5 |
2021-02-16 |
Refine default DB by adjusting how genus-level NCBI import trimmed. |
v0.7.4 |
2021-02-15 |
Edit-graph genus-only labels. New |
v0.7.3 |
2021-01-29 |
Update NCBI import, taxonomy. New |
v0.7.2 |
2020-10-06 |
New |
v0.7.1 |
2020-09-29 |
Curated Phytophthora DB minor updates. Classifier output in edit-graph. |
v0.7.0 |
2020-04-02 |
Read counts etc as a header in intermediate FASTA files; shown in reports. |
v0.6.15 |
2020-03-12 |
Fix regression in read report column sorting. |
v0.6.14 |
2020-03-12 |
Merge |
v0.6.13 |
2020-03-09 |
New classifier method |
v0.6.12 |
2020-03-09 |
New advanced setting |
v0.6.11 |
2020-03-02 |
Update genus-level only NCBI import, restrict to those with 32bp leader. |
v0.6.10 |
2020-02-24 |
Treat I (for inosine as in tRNA) in primers as N (IUPAC code for any base). |
v0.6.9 |
2020-02-20 |
Allow pre-primer-trimmed FASTQ. Fix row coloring when missing samples. |
v0.6.8 |
2020-02-17 |
Metadata |
v0.6.7 |
2020-02-13 |
Method in |
v0.6.6 |
2020-02-05 |
Coloring groups in |
v0.6.5 |
2020-01-27 |
Do |
v0.6.4 |
2020-01-23 |
|
v0.6.3 |
2020-01-20 |
Treat NCBI taxonomy “includes” as synonyms, 396 new species aliases. |
v0.6.2 |
2020-01-14 |
Memory optimisation to the default |
v0.6.1 |
2020-01-08 |
Requires at least Python 3.6 as now using f-strings (internal change only). |
v0.6.0 |
2020-01-08 |
Stop discarding normally conserved Phytophthora ITS1 marker 32bp start. |
v0.5.8 |
2019-12-11 |
Correction to start of a P. parsiana curated sequence in our DB. |
v0.5.7 |
2019-12-09 |
Replace min bit score with min percentage coverage in |
v0.5.6 |
2019-12-04 |
Import species under “unclassified Phytophthora” as genus Phytophthora. |
v0.5.5 |
2019-12-03 |
Update NCBI taxonomy, adds Phytophthora caryae and P. pseudopolonica. |
v0.5.4 |
2019-12-02 |
Only use HMM to detect synthetic read negative controls. |
v0.5.3 |
2019-11-25 |
Replace HMM filter on importing to the database with length check only. |
v0.5.2 |
2019-11-25 |
Remove redundant use of HMM filter in |
v0.5.1 |
2019-11-22 |
Update NCBI taxonomy, adds Phytophthora oreophila and P. cacuminis. |
v0.5.0 |
2019-11-21 |
Only use HMM as a filter, not for trimming in DB import or classify steps. |
v0.4.19 |
2019-11-19 |
Additional curated entries in default ITS1 database. |
v0.4.18 |
2019-11-19 |
Rework |
v0.4.17 |
2019-11-15 |
Control based minimum abundance threshold applied at folders level. |
v0.4.16 |
2019-11-15 |
Bug fix in |
v0.4.15 |
2019-11-04 |
Harmonise |
v0.4.14 |
2019-10-23 |
Configurable FASTA entry separator for |
v0.4.13 |
2019-10-22 |
Fix 5 cases missing |
v0.4.12 |
2019-10-22 |
Remove now unused |
v0.4.11 |
2019-10-21 |
Update curated DB entries, focused on truncated sequences. |
v0.4.10 |
2019-10-21 |
New |
v0.4.9 |
2019-10-17 |
New |
v0.4.8 |
2019-10-11 |
New |
v0.4.7 |
2019-10-10 |
New |
v0.4.6 |
2019-10-02 |
Forgot to include updated DB with the PyPI release. |
v0.4.5 |
2019-10-02 |
Apply primer trimming to |
v0.4.4 |
2019-10-02 |
New |
v0.4.3 |
2019-09-26 |
New |
v0.4.2 |
2019-09-26 |
Drop clade from taxonomy table, require unique species entries. |
v0.4.1 |
2019-09-16 |
Include NCBI strains/variants/etc & their synonyms as species synonyms. |
v0.4.0 |
2019-09-12 |
NCBI taxonomy synonym support; Oomycetes default taxonomy import. |
v0.3.12 |
2019-09-12 |
New |
v0.3.11 |
2019-09-09 |
Update default DB and tests to use September 2019 NCBI taxonomy. |
v0.3.10 |
2019-09-05 |
Handle missing or empty input FASTQ files more gracefully. |
v0.3.9 |
2019-08-14 |
Log BLAST bit score, merge |
v0.3.8 |
2019-08-09 |
The |
v0.3.7 |
2019-08-05 |
Add Python API to the main documentation. |
v0.3.6 |
2019-07-19 |
Add Zenodo FASTQ link to worked example and use |
v0.3.5 |
2019-07-12 |
Add missing |
v0.3.4 |
2019-07-08 |
Worked example using woody hosts dataset from Riddell et al. (2019). |
v0.3.3 |
2019-07-04 |
Fix regression in group coloring for |
v0.3.2 |
2019-07-04 |
Read The Docs; use |
v0.3.1 |
2019-06-27 |
Reformat documentation to use reStructuredText rather than Markdown. |
v0.3.0 |
2019-06-26 |
Include four gBlocks synthetic negative controls in DB and pipeline. |
v0.2.6 |
2019-06-25 |
Phytophthora ITS1 HMM threshold set within model file, not in code. |
v0.2.5 |
2019-06-21 |
Include XGMML edit-graph (for Cytoscape use) in |
v0.2.4 |
2019-06-21 |
Fix 3 Hyaloperonospora also in Peronospora in default DB. |
v0.2.3 |
2019-06-18 |
Sample count rather than total read abundance for edit-graph node size. |
v0.2.2 |
2019-06-12 |
New |
v0.2.1 |
2019-05-27 |
Cope better with multiple (short) ITS1 fragments during classification. |
v0.2.0 |
2019-05-14 |
Limit ITS1 length, 100-250bp. Exclude uncultured NCBI entries from DB. |
v0.1.12 |
2019-05-09 |
Sort |
v0.1.11 |
2019-05-06 |
Excel output from |
v0.1.10 |
2019-05-03 |
Tweak command line API, renamed |
v0.1.9 |
2019-05-02 |
New |
v0.1.8 |
2019-05-01 |
Standard errors for missing external tools. Log versions in verbose mode. |
v0.1.7 |
2019-05-01 |
Chang default classifier method from |
v0.1.6 |
2019-04-30 |
Include ready to use binary ITS1 DB in source tar-ball & wheel files. |
v0.1.5 |
2019-04-29 |
Rework optional metadata integration and its display in summary reports. |
v0.1.4 |
2019-04-25 |
Sort samples using the optional metadata fields requested in reports. |
v0.1.3 |
2019-04-24 |
Can optionally display sample metadata from TSV file in summary reports. |
v0.1.2 |
2019-04-17 |
Keep searching if |
v0.1.1 |
2019-04-16 |
Expand default taxonomy & DB from Peronosporaceae to Peronosporales. |
v0.1.0 |
2019-04-04 |
Include a bundled ITS1 DB. |
v0.0.15 |
2019-04-03 |
Support for genus-level only entries in the DB. |
v0.0.14 |
2019-04-01 |
MD5 in dump output. Fix importing sequences failing taxonomic validation. |
v0.0.13 |
2019-03-22 |
Drop conserved 32bp when primer trim. Assess at sample level by default. |
v0.0.12 |
2019-03-11 |
Fix bug in |
v0.0.11 |
2019-03-08 |
Sped up FASTQ preparation by using |
v0.0.10 |
2019-03-06 |
Replace primer code allowing only 1bp differences with |
v0.0.9 |
2019-03-05 |
Look for expected primers, discards mismatches. Cache HMM files locally. |
v0.0.8 |
2019-02-21 |
Fix multi-class TN under-counting. New loss metric, |
v0.0.7 |
2019-02-12 |
New |
v0.0.6 |
2019-02-07 |
Misc. cleanup and import fixes. |
v0.0.5 |
2019-02-06 |
Hamming Loss in assessment output. |
v0.0.4 |
2019-01-24 |
New |
v0.0.3 |
2019-01-22 |
Simplify generated filenames. |
v0.0.2 |
2019-01-21 |
New |
v0.0.1 |
2019-01-17 |
Initial framework with |