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Merge pull request #74 from kbessonov1984/master
ecTyper version 0.9.0 with improved reporting and O-antigen call rate
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**v0.8.1** | ||
* supports E.coli species detection via 10 short 1000 bp sequences based on E.coli core genomes | ||
* contains signatures for the 178 O and 53 H antigen types | ||
* non-E.coli isolates are identified using mash screen function against entire RefSeq database of all genomes | ||
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**v0.9.0** | ||
* improved O-antigen serotyping coverage of complex samples that lack some O-antigen signatures. | ||
* fall back to single O-antigen signature detection when both signature pairs are not found and species is E.coli | ||
* improved O-antigen identification favoring presence of both alleles (e.g. wzx and wzy) to support the final call. | ||
The sum of scores for both alleles of the same antigen is used in ranking now | ||
* verification for E.albertii species against RefSeq genomes | ||
* addition of Quality Control flags in the output (as an extra column in the `results.tsv`) for ease of results interpretation | ||
* species reporting to better resolve E.coli vs Shigella vs E.albertii cases and contamination | ||
* serotype prediction for all Escherichia genus to ease classification of cryptic spqeices | ||
* automatic download of the RefSeq sketch and associated meta data every 6 months for improved species identification | ||
* improved species identification for the FASTQ files. All raw reads are used for species identification | ||
* better complex cases handling and error recovery in cases of poor reference allele coverage. | ||
* serotype reporting based on multiple evidences including reference allele database and closest reference genome | ||
* query length coverage default threshold lowered from 50% to 10% for truncated alleles. This greatly improved sensitivity. | ||
Did not found any noticeable negative effect on specificity and accuracy based on EnteroBase, PNC2018-2019 and internal datasets | ||
* users is warned about potential false postive result in case of non-E.coli species or assembly errors | ||
* wrote additional unit tests | ||
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__version__ = "0.8.1" | ||
__version__ = "0.9.0" |
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