SeqSphere+ Program

  • Ridom SeqSphere+ version 7.7 (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 2.3.0 (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 3.11.1 (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 (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 (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 0.11.7 (quality control for raw sequence data; GPL v3)
    https://www.bioinformatics.babraham.ac.uk/projects/fastqc

  • 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, Phillippy AM. Mash Screen: High-throughput sequence containment estimation for genome discovery. bioRxiv. 2019 Mar. doi: 10.1101/557314 [bioRxiv]

  • 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 (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 2.17.6 (SAM/BAM file processing; MIT license)
    https://broadinstitute.github.io/picard

  • Illumina InterOp Utilities (Reading Illinuma InterOp files; GPL v3)
    https://github.com/Illumina/interop

  • NCBI SRA Toolkit version 2.9.6 (Downloading reads from NCBI SRA; Public domain)
    https://github.com/ncbi/sra-tools

  • Samtools version 1.7 (SAM/BAM file processing; The 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]

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]

Geographical Map Sources