SeqSphere+ Program

  • Ridom SeqSphere+ version 6.1 (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: 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: 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: 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: 821-9 [PubMed 18349386]

  • BWA-SW version 0.6.2 (de novo assembly; GPL v3)
    Li H, and Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010, 26: 589-95: 589-95 [PubMed 20080505]

  • 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: 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: 2114-20 [PubMed 24695404]

  • 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

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: 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; term of use)
    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: D36-D40 [PubMed 29140475]

  • NCBI Genome Database and Sequence Read Archive (SRA) (download of genomes and raw reads; policies)
    NCBI Resource Coordinators . Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2018, 46: D8-D13: D8-D13 [PubMed 29140470]

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

Geographical Map Sources