v2.0.0: Pathotyping and Shiga toxin typing

• Updated species identification module now based on GTDB + custom Escherichia and Shigella sketch covering all known bacterial species
• Implemented pathotyping covering 7 DEC Escherichia coli pathotypes (DAEC, EAEC, EHEC, EIEC, EPEC, ETEC and STEC) supporting simultaneous presence of multiple signatures (e.g. ETEC/STEC). Note that EHEC is reported as EHEC-STEC as this is a more severe subtype of STEC.
• Implemented Shiga 1 and 2 toxin typing supporting multiple toxin signatures present in a single sample.
  • A total of 4 stx1 subtypes are supported: stx1a, stx1c, stx1d and stx1e.
  • A total of 15 stx2 subtypes are supported: stx2a, stx2b, stx2c, stx2d, stx2e, stx2f, stx2g ,stx2h, stx2i, stx2j, stx2k, stx2l, stx2m, stx2n, stx2o.
• new database of pathotypes and toxins in JSON clear transparent format composed of the key virulence factors based on both BioNumerics and literature sources
• support for gzip compressed inputs fastq.gz and fasta.gz saving storage and increasing versatility
• other toxin typing covering enterohemolysin A (ehxA), hemolysin E (hlyE), hemolysin A (hlyA)
• support for long raw reads improving mapping capabilities of bowtie2