assemblers

bioboxes/velvet

The velvet assembler was one of the first assemblers created for short read sequencing. Velvet was developed at the European Bioinformatics Institute.

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Version: 1.2.10
Sha256:

6611675a6d3755515592aa71932bd4ea4c26bccad34fae7a3ec1198ddcccddad

Tasks:
  • default
  • careful

    • bioboxes/megahit

    MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner, it is developed in the department of Computer Science at the University of Hong Kong.

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    Version: 1.0.6
    Sha256:

    b6bc1475be3ff72b26e23903dfae24ceded227167ae7363b80954b11906deac7

    Tasks:
    • default
    • no-mercy

      • bioboxes/idba

      IDBA (iterative De Bruijn Graph De Novo Assembler) is developed by the Bioinfomatics Research Group in the department of Computer Science at the University of Hong Kong.

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      Version: 1.0.9
      Sha256:

      c97b741e992cb9cf82ff2f9c44673be2a914ac5c2cd20fa2e4975864cce09473

      Tasks:
      • default
      • single-cell
      • idba

        • bioboxes/soap

        The short oligonucleotide analysis package (SOAP) is developed by BGI HK Research Institute in Hong Kong.

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        Version: 2.04
        Sha256:

        16d6dc4d076088ab1af97d4bbf9f052a54f6d51f4b0221fb93844013eccdda68

        Tasks:
        • default

          • bioboxes/sparse

          SparseAssembler utilises a sparse k-mer graph structure evolved from the de Bruijn graph and is developed at the Chinese Academy of Sciences in Menglun.

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          Version: 17.08.2012
          Sha256:

          3483ddcd1e4b1a91ceb24d8e7d085eaa51ea6354560cf5e455baa77c2b8ffb40

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          • careful

            • bioboxes/sga

            De novo sequence assembler using string graphs developed at the Wellcome Trust Sanger Institute in the UK.

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            Version: v0.10.13
            Sha256:

            3dda6c28b5843af51c53344f1309f8a21358292539233408b130baedc849556f

            Tasks:
            • default
            • careful

              • bioboxes/minia

              Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Minia is developed at the IRISA institute in France.

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              Version: 1.6906
              Sha256:

              f1d8384b229a38351528d321f148210e1eee417204b6265e538fa2f776b25253

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              • default

                • bioboxes/ray

                Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.

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                Version: 2.3.0
                Sha256:

                faa7f64683ae2e9d364127a173dadb6a42f9fe90799625944cfcadb27fdd5a29

                Tasks:
                • default

                  • bioboxes/velour

                  Velour is a memory efficient short read de novo DNA sequence assembly tool for gigabase-scale genomes.

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                  Version: 4669239608655289e2538ea69161dad433ab5fbf
                  Sha256:

                  fb000d39755a008f265dc871bbe3d741e36f97445f385ab99206888f8ac705dd

                  Tasks:
                  • default
                  • fast
                  • fast2
                  • faster
                  • faster2