MBioSEQ Ridom Typer Program

  • MBioSEQ Ridom Typer version 12.0 (EULA)
    Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, and Harmsen D. Updating benchtop sequencing performance comparison. Nat Biotechnol. 2013, 31: 294-6 [PubMed 23563421]

  • Long Read Plasmid Transmission
    Scherff N, Rothgänger J, Weniger T, Mellmann A, and Harmsen D. Real-time plasmid transmission detection pipeline. Microbiol Spectr. 2024, 12: e0210024 [PubMed 39470278]

  • Long Read Assembly with proprietary ONT-cgMLST-Polisher
    Prior K, Becker K, Brandt C, Cabal Rosel A, Dabernig-Heinz J, Kohler C, Lohde M, Ruppitsch W, Schuler F, Wagner GE, and Mellmann A. Accurate and reproducible whole-genome genotyping for bacterial genomic surveillance with Nanopore sequencing data. J Clin Microbiol. 2025, 63: e0036925 [PubMed 40511924]

Other Programs

Programs are invoked via command line and standard output is read.

  • SKESA version 2.4.0 (de novo assembly; GPL v3; source code unmodified)
    Souvorov A, Agarwala R, and Lipman DJ. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol. 2018, 19: 153 [PubMed 30286803]

  • SPAdes version 4.2.0 (de novo assembly; GPL v2; source code unmodified)
    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, and Pevzner PA. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012, 19: 455-77 [PubMed 22506599]

  • Velvet version 1.1.04 (de novo assembly; GPL v2; source code unmodified)
    Zerbino DR, and Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18: 821-9 [PubMed 18349386]

  • BWA-SW version 0.6.1 (reference-assisted assembly; GPL v3; source code unmodified)
    Li H, and Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010, 26: 589-95 [PubMed 20080505]

  • BWA-MEM version 0.7.15 (reference-assisted assembly; GPL v3; source code unmodified)
    Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. 2013. arXiv:1303.3997 [q-bio.GN] [arXiv]

  • FastQC version 0.11.9 (Quality control for raw sequence data; GPL v3; source code unmodified)
    https://www.bioinformatics.babraham.ac.uk/projects/fastqc

  • Mash Distance version 2.1 (species identification; BSD license; source code unmodified)
    Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, and Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016, 17: 132 [PubMed 27323842]

  • Mash Screen version 2.1 (inter-species contamination check; BSD license; source code unmodified)
    Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, and Phillippy AM. Mash Screen: high-throughput sequence containment estimation for genome discovery. Genome Biol. 2019, 20: 232 [PubMed 31690338]

  • Trimmomatic version 0.36 (Illumina adapter trimming; GPL v3; source code unmodified)
    Bolger AM, Lohse M, and Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014, 30: 2114-20 [PubMed 24695404]

  • NCBI AMRFinderPlus version 4.0.15 (Identifying resistance/virulence genes using BLASTX search; Public domain; source code unmodified)
    Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu CH, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, and Klimke W. Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. Antimicrob Agents Chemother. 2019, 63 [PubMed 31427293]

  • Picard version 2.17.11 (SAM/BAM file processing; MIT license; source code unmodified)
    https://broadinstitute.github.io/picard

  • Illumina InterOp Utilities version 1.3.1 (Reading Illinuma InterOp files; GPL v3; source code unmodified)
    https://github.com/Illumina/interop

  • NCBI SRA Toolkit version 3.0.10 (downloading reads from NCBI SRA; Public domain; source code unmodified)
    https://github.com/ncbi/sra-tools

  • Samtools version 1.22.1 (SAM/BAM file processing; MIT/Expat license; source code unmodified)
    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, and Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25: 2078-9 [PubMed 19505943]

  • iVar version 1.3.1 (tiled amplicon primer trimming and consensus calling; GPL v3; source code unmodified)
    Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, and Andersen KG. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biol. 2019, 20: 8 [PubMed 30621750]

  • Pangolin (assigning SARS-CoV-2 PANGO lineage; GPL v3; source code unmodified)
    Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, and Pybus OG. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020, 5: 1403-1407 [PubMed 32669681]

  • IGV (viewing BAM files; MIT license; source code unmodified)
    Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, and Mesirov JP. Integrative genomics viewer. Nat Biotechnol. 2011, 29: 24-6 [PubMed 21221095]

  • MOB-suite version 3.1.8 (clustering, reconstruction and typing of plasmids; Apache license 2.0; source code unmodified)
    Robertson J, and Nash JHE. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom. 2018, 4 [PubMed 30052170]

  • MobileElementFinder version 1.1.2 (identifying Mobile Genetic Elements (MGE); GPL v3; modified source code)
    Johansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP, and Petersen TN. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother. 2021, 76: 101-109 [PubMed 33009809]

  • SISTR version 1.1.3 (Salmonella In Silico Typing Resource (SISTR); Apache license 2.0; source code unmodified)
    Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VP, Nash JH, and Taboada EN. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PLoS One. 2016, 11: e0147101 [PubMed 26800248]

  • FastANI version 3.1.8 (whole-genome Average Nucleotide Identity; Apache license 2.0; source code unmodified)
    Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, and Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018, 9: 5114 [PubMed 30504855]

  • pyGenomeViz (genome visualization python package; MIT License; source code unmodified)
    https://moshi4.github.io/pyGenomeViz/

  • TB-Profiler version 6.6.6 (M. tuberculosis AMR and linage; GPL v3; source code unmodified)
    Phelan JE, O'Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino S, O'Grady J, McNerney R, Hibberd ML, Viveiros M, Huggett JF, and Clark TG. Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med. 2019, 11: 41 [PubMed 31234910]

  • MUMmer (sequence alignment; Artistic License 1.0; source code unmodified)
    Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, and Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 2004, 5: R12 [PubMed 14759262]

  • GrapeTree (calculating and viewing large MSTs; GPL v3; source code unmodified)
    Zhou Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, Carriço JA, and Achtman M. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res. 2018, 28: 1395-1404 [PubMed 30049790]

  • Chopper (long read quality trimming; MIT license; source code unmodified)
    De Coster W, and Rademakers R. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics. 2023, 39 [PubMed 37171891]

  • Rasusa version 0.8.0 (long read downsampling; MIT license; source code unmodified)
    Michael B. Hall. Rasusa: Randomly subsample sequencing reads to a specified coverage. JOSS. 2022 Jan. doi: 10.21105/joss.03941 [JOSS]

  • Filtlong (long read downsampling; GPL v3; source code unmodified)
    https://github.com/rrwick/Filtlong

  • Flye​ version 2.9.3-b1797 (long read assembling; 3-Clause BSD license; source code unmodified)
    Kolmogorov M, Yuan J, Lin Y, and Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019, 37: 540-546 [PubMed 30936562]

  • Raven​ version 1.8.3 (long read assembling; MIT license; source code unmodified)
    Vaser R, and Šikić M. Time- and memory-efficient genome assembly with Raven. Nat Comput Sci. 2021, 1: 332-336 [PubMed 38217213]

  • Minimap2​ version 2.28-r1209 (long read mapping; MIT license; source code unmodified)
    Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018, 34: 3094-3100 [PubMed 29750242]

  • Medaka​ version 2.0.1 (long read assembly polishing; Mozilla Public License Version 2.0; source code unmodified)
    Oxford Nanopore Technologies

  • CheckM2 version 1.1.0 (contamination check; GPL v3; source code unmodified)
    Chklovski A, Parks DH, Woodcroft BJ, and Tyson GW. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods. 2023, 20: 1203-1212 [PubMed 37500759]

  • GAMBIT version 1.1.0 (species identification; GNU Affero General Public License v3.0; source code unmodified)
    Lumpe J, Gumbleton L, Gorzalski A, Libuit K, Varghese V, Lloyd T, Tadros F, Arsimendi T, Wagner E, Stephens C, Sevinsky J, Hess D, and Pandori M. GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification. PLoS One. 2023, 18: e0277575 [PubMed 36795668]

Java Runtime Environment

Dynamically Loaded C Library

  • BLAST version 2.2.12 (Public domain)
    Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-402 [PubMed 9254694]

Dynamically Loaded Java Libraries

For the list of Java libaries that are used in MBioSEQ Ridom Typer see menu Help | Citations and Licenses.
 

Sequence Databases

  • European Nucleotide Archive (ENA) (Upload of raw reads; policy)
    Silvester N, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Harrison PW, Jayathilaka S, Kay S, Keane T, Leinonen R, Liu X, Martínez-Villacorta J, Menchi M, Reddy K, Pakseresht N, Rajan J, Rossello M, Smirnov D, Toribio AL, Vaughan D, Zalunin V, and Cochrane G. The European Nucleotide Archive in 2017. Nucleic Acids Res. 2018, 46: D36-D40 [PubMed 29140475]

  • NCBI Genomes/Datasets and Sequence Read Archive (SRA) (Download of genomes and raw reads; policy)
    Sayers EW, Beck J, Bolton EE, Bourexis D, Brister JR, Canese K, Comeau DC, Funk K, Kim S, Klimke W, Marchler-Bauer A, Landrum M, Lathrop S, Lu Z, Madden TL, O'Leary N, Phan L, Rangwala SH, Schneider VA, Skripchenko Y, Wang J, Ye J, Trawick BW, Pruitt KD, and Sherry ST. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2021, 49: D10-D17 [PubMed 33095870]

  • PubMLST (Download of MLST schemes; policy)
    Jolley KA, and Maiden MC. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010, 11: 595 [PubMed 21143983]

  • BIGSdb-Pasteur (Download of MLST schemes; policy)
    We thank the Institut Pasteur teams for the curation and maintenance of BIGSdb-Pasteur databases at http://bigsdb.pasteur.fr/

  • CGE SerotypeFinder (E. coli serotyping scheme; policy)
    Joensen KG, Tetzschner AM, Iguchi A, Aarestrup FM, and Scheutz F. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data. J Clin Microbiol. 2015, 53: 2410-26 [PubMed 25972421]

  • GISAID (Submission of SARS-CoV-2 contigs and metadata; policy)
    Elbe S, and Buckland-Merrett G. Data, disease and diplomacy: GISAID's innovative contribution to global health. Glob Chall. 2017, 1: 33-46 [PubMed 31565258]

  • Circlator dnaA database (Fix Start and Orientation for Plasmids or Chromosomes; GPL v3)
    Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, and Harris SR. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 2015, 16: 294 [PubMed 26714481]

  • ShigaPass ipaH/MLST databases (Differentiate between E. coli and Shigella; GPL v3)
    https://github.com/imanyass/ShigaPass/tree/main/SCRIPT/ShigaPass_DataBases

  • Thiagen GAMBIT database version 2.0.1 (Reference database for GAMBIT; GPL v3)
    https://theiagen.github.io/public_health_bioinformatics/latest/guides/gambit/#gambit-databases

  • LTP version LTP_10_2024 (Reference database for 16S rRNA; CC BY 4.0)
    Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, and Rosselló-Móra R. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol. 2008, 31: 241-50 [PubMed 18692976]

  • UNITE version 10.0 2025-02-19 (Reference database for ITS; CC BY 4.0)
    Abarenkov K, Nilsson RH, Larsson KH, Taylor AFS, May TW, Frøslev TG, Pawlowska J, Lindahl B, Põldmaa K, Truong C, Vu D, Hosoya T, Niskanen T, Piirmann T, Ivanov F, Zirk A, Peterson M, Cheeke TE, Ishigami Y, Jansson AT, Jeppesen TS, Kristiansson E, Mikryukov V, Miller JT, Oono R, Ossandon FJ, Paupério J, Saar I, Schigel D, Suija A, Tedersoo L, and Kõljalg U. The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered. Nucleic Acids Res. 2024, 52: D791-D797 [PubMed 37953409]

  • TB-Profiler database version WHO catalogue v2 + tbdb (Database for TB-Profiler AMR ; GPL v3)
    Phelan JE, O'Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino S, O'Grady J, McNerney R, Hibberd ML, Viveiros M, Huggett JF, and Clark TG. Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med. 2019, 11: 41 [PubMed 31234910]

Geographical Map Sources

 
FOR RESEARCH USE ONLY. NOT FOR USE IN CLINICAL DIAGNOSTIC PROCEDURES.