SeqSphere+ Program

  • Ridom SeqSphere+ version 10.0 (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]

Other Programs

Programs are invoked via command line and standard output is read. Source codes of programs were not modified by Ridom.

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

  • SPAdes version 3.15.4 (de novo assembly; GPL v2)
    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; modified source)
    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 0.6.2 (reference-assisted assembly; GPL v3)
    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)
    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)

  • Mash Distance version 2.1 (species identification; BSD license)
    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 (contamination check; BSD license)
    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)
    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 3.11.26 (Identifying resistance/virulence genes using BLASTX search; Public domain)
    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)

  • Illumina InterOp Utilities version 1.1.4 (Reading Illinuma InterOp files; GPL v3)

  • NCBI SRA Toolkit version 3.0.10 (Downloading reads from NCBI SRA; Public domain)

  • Samtools version 1.19.2 (SAM/BAM file processing; MIT/Expat license)
    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)
    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)
    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)
    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)
    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)
    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 1.1.1 (Salmonella In Silico Typing Resource (SISTR); Apache license 2.0)
    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)
    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 version 0.4.4 (Genome visualization python package; MIT License)

  • MUMmer (Software system for sequence alignment; Artistic License 1.0)
    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)
    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)
    De Coster W, and Rademakers R. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics. 2023, 39 [PubMed 37171891]

  • Rasusa (Long read downsampling; MIT license)
    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)

  • Flye​ (Long read assembling; 3-Clause BSD license)
    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​ (Long read assembling; MIT license)
    Vaser R, and Šikić M. Time- and memory-efficient genome assembly with Raven. Nat Comput Sci. 2021, 1: 332-336 [PubMed 38217213]

  • Medaka​ (Long read assembly polishing; Mozilla Public License Version 2.0)
    Oxford Nanopore Technologies

Java Runtime Environment

Dynamically Loaded 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 Ridom SeqSphere+ 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 Genome Database and Sequence Read Archive (SRA) (Download of genomes and raw reads; policy)
    NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2018, 46: D8-D13 [PubMed 29140470]

  • 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]

  • 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]

  • VFDB (Virulence schemes; policy)
    Chen L, Zheng D, Liu B, Yang J, and Jin Q. VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on. Nucleic Acids Res. 2016, 44: D694-7 [PubMed 26578559]

  • 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)

Geographical Map Sources