References

SSI analysis employs different tools and algorithms that are described in academic publications. Here we attach the complete list:

AMRFinder

Feldgarden, Michael, et al. "AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence." Scientific reports 11.1 (2021): 12728.

BLAST

Camacho, Christiam, et al. "ElasticBLAST: accelerating sequence search via cloud computing." BMC bioinformatics 24.1 (2023): 117.

Boratyn, Grzegorz M., et al. "Magic-BLAST, an accurate RNA-seq aligner for long and short reads." BMC bioinformatics 20.1 (2019): 405.

Boratyn, Grzegorz M., et al. "Domain enhanced lookup time accelerated BLAST." Biology direct 7.1 (2012): 12.

Camacho, Christiam, et al. "BLAST+: architecture and applications." BMC bioinformatics 10.1 (2009): 421.

Morgulis, Aleksandr, et al. "Database indexing for production MegaBLAST searches." Bioinformatics 24.16 (2008): 1757-1764.

Zhang Z., Schwartz S., Wagner L., Miller W. (2000), “A greedy algorithm for aligning DNA sequences” J Comput Biol 2000; 7(1-2):203-14

Altschul, Stephen F., et al. "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic acids research 25.17 (1997): 3389-3402.

Altschul, Stephen F., et al. "Basic local alignment search tool." Journal of molecular biology 215.3 (1990): 403-410.

Bowtie2

Langmead, Ben, et al. "Scaling read aligners to hundreds of threads on general-purpose processors." Bioinformatics 35.3 (2019): 421-432.

Langmead, Ben, and Steven L. Salzberg. "Fast gapped-read alignment with Bowtie 2." Nature methods 9.4 (2012): 357-359.

Langmead, Ben, et al. "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome." Genome biology 10.3 (2009): R25.

HTSlib

Bonfield, James K., et al. "HTSlib: C library for reading/writing high-throughput sequencing data." Gigascience 10.2 (2021): giab007.

Kleborate

Lam, Margaret MC, et al. "A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex." Nature communications 12.1 (2021): 4188.

kma

Clausen, Philip TLC, et al. "Assembly-free typing of Nanopore and Illumina data through proximity scoring with KMA." NAR Genomics and Bioinformatics 7.3 (2025): lqaf116.

Clausen, Philip TLC, Frank M. Aarestrup, and Ole Lund. "Rapid and precise alignment of raw reads against redundant databases with KMA." BMC bioinformatics 19.1 (2018): 307.

MeningoType

Kwong JC, Gonçalves da Silva A, Stinear TP, Howden BP, Seemann T. meningotype: in silico typing for Neisseria meningitidis. GitHub https://github.com/MDU-PHL/meningotype

Minimap2

Li, Heng. "New strategies to improve minimap2 alignment accuracy." Bioinformatics 37.23 (2021): 4572-4574.

Li, Heng. "Minimap2: pairwise alignment for nucleotide sequences." Bioinformatics 34.18 (2018): 3094-3100.

MLST

Seemann T, mlst Github https://github.com/tseemann/mlst

PlasmidFinder

Carattoli, Alessandra, et al. "PlasmidFinder and pMLST: in silico detection and typing of plasmids." Antimicrob Agents Chemother 58.7 (2014): 3895-903.

ResFinder

Florensa, Alfred Ferrer, et al. "ResFinder–an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes." Microbial genomics 8.1 (2022): 000748.

Bortolaia, Valeria, et al. "ResFinder 4.0 for predictions of phenotypes from genotypes." Journal of Antimicrobial Chemotherapy 75.12 (2020): 3491-3500.

SeqSero2

Zhang, Shaokang, et al. "SeqSero2: rapid and improved Salmonella serotype determination using whole-genome sequencing data." Applied and environmental microbiology 85.23 (2019): e01746-19.

Zhang, Shaokang, et al. "Salmonella serotype determination utilizing high-throughput genome sequencing data." Journal of clinical microbiology 53.5 (2015): 1685-1692.

SerotypeFinder

Clausen, Philip TLC, Frank M. Aarestrup, and Ole Lund. "Rapid and precise alignment of raw reads against redundant databases with KMA." BMC bioinformatics 19.1 (2018): 307.

Shovill

Seemann T (2016) Shovill Github https://github.com/tseemann/shovill

SISTR

Yoshida, Catherine E., et al. "The Salmonella in silico typing resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies." PloS one 11.1 (2016): e0147101.

spaTyper

Bartels, Mette Damkjær, et al. "Comparing whole-genome sequencing with Sanger sequencing for spa typing of methicillin-resistant Staphylococcus aureus." Journal of clinical microbiology 52.12 (2014): 4305-4308.

VirulenceFinder

Scheutz, Flemming, Camilla Hald Nielsen, and Astrid von Mentzer. "Construction of the ETECFinder database for the characterization of enterotoxigenic Escherichia coli (ETEC) and revision of the VirulenceFinder web tool at the CGE website." Journal of Clinical Microbiology 62.6 (2024): e00570-23.

Lindsey, Rebecca L., et al. "Identification and characterization of ten Escherichia coli strains encoding novel Shiga toxin 2 subtypes, Stx2n as well as Stx2j, Stx2m, and Stx2o, in the United States." Microorganisms 11.10 (2023): 2561.

Gill, Alexander, et al. "Characterization of atypical Shiga toxin gene sequences and description of Stx2j, a new subtype." Journal of clinical microbiology 60.3 (2022): e02229-21.

Malberg Tetzschner, Anna Maria, et al. "In silico genotyping of Escherichia coli isolates for extraintestinal virulence genes by use of whole-genome sequencing data." Journal of clinical microbiology 58.10 (2020): 10-1128.

Joensen, Katrine Grimstrup, et al. "Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli." Journal of clinical microbiology 52.5 (2014): 1501-1510.