Overview of genome characterization toolsa

Analysis tool (reference[s])Concept(s)Input type(s)Input format(s)Output format(s)Web address
    Web based
        KmerFinder (121, 122)Uses k-mers to identify strain using WGS dataRaw sequences, contigsFASTQ, FASTATab delimited, online
        NCBI BLASTb (123)NCBI Web-based interface for performing BLAST searches; searches hits in the database that match the given sequenceContigsFASTAOnline, tab delimited
        MLST Web server (125)Web-based database that identifies STs from short sequencing reads or draft genomesRaw sequences, contigsFASTQ, FASTAOnline
    Command line
        PathoScope 2.0 (127)Complete framework based on Bayesian missing-data approach, for direct strain identificationRaw sequencesFASTQ, FASTATab delimited
    Web based
        RAST (129)Web-based server for localization and identification of tRNA, rRNA, and coding sequences; includes a browser for screening the outputContigsFASTAGenBank, EMBL, GFF3, GTF, Excel, and tab delimited
    Command line
        PROKKA (132)Rapid annotation tool for localization and identification of rRNA, tRNA, tmRNA, signal peptides, noncoding RNA, and coding sequencesContigsFASTAFASTA, tab delimited, SQN, GenBank file, GFF3
    Web based
        VirulenceFinderDetect virulence genes in WGS data using the BLAST algorithmRaw sequences, contigsFASTQ, FASTATab-delimited summary, FASTA
        VFDB (138)Source of virulence information, including Web-based service to perform BLAST to detect virulence genesContigsFASTAOnline, tab delimited
Antimicrobial resistance
    Web based
        ResFinderDetects resistance genes in WGS dataRaw sequences, contigsFASTQ, FASTATab-delimited summary, FASTA
        RGI/CARD (144146)Web-based as well as command line versions available to perform resistance gene detection using the CARD databaseContigs, GenBank accession no.FASTA, GenBank accession no. (nucleotide or protein)JSON, tab-delimited summary, FASTA, heat map PDF
        PlasmidFinderTool to detect plasmids in WGS dataRaw sequences, contigsFASTQ, FASTATab-delimited summary, FASTA
        CGE BAP (107)Web-based suite for automated genomic characterization; if raw sequence reads are provided, performs assembly; set of tools is applied to the contigs, ResFinder, VirulenceFinder, and PlasmidFinderRaw sequences, contigsFASTQ, FASTATab-delimited summaries, FASTA
  • a ND, no data; NA, not applicable; EMBL, sequence file format; JSON, JavaScript Object Notation; SQN, GenBank submission file; GFF3, General Feature Format 3.

  • b Also available as a command line tool and as GUI via prfectBLAST (124).