tools

v0 software

1. Assembly (raw input only)
   a. shovill v1.1.0 settings: --trim ( - BWA MEM - FLASh - KMC - Lighter - pigz - Pilon - samclip - SAMtools - seqtk - SPAdes - Trimmomatic - Velvet )
   b. SKESA for determining small novel plasmids
2. Annotation (raw input or contig input)
   a. PlasmidFinder v2020-02-07 settings: -t 0.9 -l 0.8 -mp blastn
   b. MLST v2023-02-06 default settings (run for both species when the GEAbash -t option is set to both)
   c. SerotypeFinder v2018-09-24 for E. coli. Settings: -t 0.95 -l 0.8
   d. SeqSero2 v1.1 for Salmonella. Settings: -m k
   e. ResFinder v4.3 settings: -acq -c -t 0.9 -l 0.8 -t_p 0.9 -l_p 0.8 -b blastn
   f. BLAST+ v2.12 (blastn) to search against the 5loci database v2023-04-28. Settings: -task megablast -outfmt '6 std'.
   g. VirulenceFinder v2020-02-06 for E. coli. Settings: -mp blastn -t 0.95 -l 0.80
   h. Ezclermont v0.7 for E. coli with default settings.
   i. FimTyper v1.1 for E. coli. Settings: -k '95.0' -l 0.8
   j. stats.sh v2020-03-03

v1 changes

additions

1. Pre-assembly
   a. seqkit v2.1.0. fq2fa, sort, head, and stats tools are used to size select down sample long sequencing reads to retain the longest n reads where n is set by the user. Default 16000
2. Assembly
   a. Flye v2.9.4 settings: --user specified input type ( - intervaltree - lemon - libcuckoo - minimap2 - samtools )

upgrades

1. Assembly
   • SPAdes. v4.0.0 upgraded from v3.15. The default assembler used by shovill.
2. Annotation

• major version upgrades
  • VirulenceFinder v3.0.1. Settings change: -b blastn
• minor version upgrades
  • ResFinder v4.6.0
  • SeqSero2 v1.3.1