E.coli serotyping with ability to differentiate between Shigella and other Escherichia cryptic species

• improved O-antigen serotyping coverage of complex samples that lack some O-antigen signatures
• better complex cases handling and error recovery in cases of poor reference allele coverage
• improved O-antigen identification precision favoring the 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
• automatic download and update of RefSeq genome sketches every 6 months
• addition of Quality Control flags in the output (as an extra column in the results.tsv) for ease of results interpretation
• improved species identification for the FASTQ files. All raw reads are used for species identification
• query length coverage default threshold lowered from 50% to 10% to account for truncated alleles. This greatly improved the sensitivity of the tool while not changing significantly specificity
• wrote additional unit tests to cover all aspects of the program
• file lock application when updating RefSeq sketch and assembly stats files