images.yml

---
assemblers:
  -
    image:
      dockerhub: bioboxes/velvet
      repo: https://github.com/bioboxes/velvet
      source: https://github.com/dzerbino/velvet
      versions:
        - tasks: ["default", "careful"]
          sha256: 6611675a6d3755515592aa71932bd4ea4c26bccad34fae7a3ec1198ddcccddad
          name: "1.2.10"
    pmids: [18349386]
    homepage: https://www.ebi.ac.uk/~zerbino/velvet/
    mailing_list: http://listserver.ebi.ac.uk/mailman/listinfo/velvet-users
    description:
      The velvet assembler was one of the first assemblers created for short read sequencing. Velvet was developed at the European Bioinformatics Institute.
  -
    image:
      dockerhub: bioboxes/megahit
      repo: https://github.com/bioboxes/megahit
      source: https://github.com/voutcn/megahit
      versions:
        - sha256: b6bc1475be3ff72b26e23903dfae24ceded227167ae7363b80954b11906deac7
          name: "1.0.6"
          tasks: ["default", "no-mercy"]
    pmids: [25609793]
    homepage:
    description: >
      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.
  -
    image:
      dockerhub: bioboxes/idba
      repo: https://github.com/bioboxes/idba
      source: https://code.google.com/p/hku-idba/
      versions:
        - sha256: c97b741e992cb9cf82ff2f9c44673be2a914ac5c2cd20fa2e4975864cce09473
          name: "1.0.9"
          tasks: ["default", "single-cell", "idba"]
    pmids: [22495754]
    homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba/
    mailing_list: https://groups.google.com/forum/#!forum/hku-idba
    description: >
      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.
  -
    image:
      dockerhub: bioboxes/soap
      repo: https://github.com/bioboxes/soap
      source: http://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/
      versions:
        - name: "2.04"
          tasks: ["default"]
          sha256: 16d6dc4d076088ab1af97d4bbf9f052a54f6d51f4b0221fb93844013eccdda68
    pmids: [23587118]
    homepage: http://soap.genomics.org.cn/soapdenovo.html
    mailing_list: https://groups.google.com/forum/#!forum/bgi-soap
    description: >
      The short oligonucleotide analysis package (SOAP) is developed by BGI HK Research Institute in Hong Kong.
  -
    image:
      dockerhub: bioboxes/sparse
      repo: https://github.com/bioboxes/sparse
      source: http://sourceforge.net/projects/sparseassembler/
      versions:
        - name: "17.08.2012"
          tasks: ["default", "careful"]
          sha256: 3483ddcd1e4b1a91ceb24d8e7d085eaa51ea6354560cf5e455baa77c2b8ffb40
    pmids: [22537038]
    homepage: https://sites.google.com/site/sparseassembler/
    mailing_list:
    description: >
      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.
  - 
    image:
      dockerhub: bioboxes/sga
      repo: https://github.com/bioboxes/sga
      source: https://github.com/jts/sga
      versions:
        - tasks: ["default", "careful"]
          name: "v0.10.13"
          sha256: 3dda6c28b5843af51c53344f1309f8a21358292539233408b130baedc849556f
    pmids: [22156294]
    homepage: https://github.com/jts/sga/wiki
    mailing_list: https://groups.google.com/forum/#!forum/sga-users
    description: >
      De novo sequence assembler using string graphs developed at the Wellcome Trust Sanger Institute in the UK.
  -
    image:
      dockerhub: bioboxes/minia
      repo: https://github.com/rchikhi/docker-minia
      source:
      versions:
        - tasks: ["default"]
          name: "1.6906"
          sha256: f1d8384b229a38351528d321f148210e1eee417204b6265e538fa2f776b25253
    pmids: [24040893]
    homepage: http://minia.genouest.org/
    mailing_list: https://www.biostars.org/t/minia/
    description: >
      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.
  -
    image:
      dockerhub: bioboxes/ray
      repo: https://github.com/sebhtml/ray
      source:
      versions:
        - tasks: ["default"]
          sha256: faa7f64683ae2e9d364127a173dadb6a42f9fe90799625944cfcadb27fdd5a29
          name: "2.3.0"
    pmids: [20958248]
    homepage: http://gatb.inria.fr/
    mailing_list: https://www.biostars.org/t/gatb/
    description: >
      Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.
  -
    image:
      dockerhub: bioboxes/velour
      repo: https://github.com/bioboxes/velour
      source: https://github.com/jjcook/velour
      versions:
        - tasks: ["default", "fast", "fast2", "faster", "faster2"]
          name: "4669239608655289e2538ea69161dad433ab5fbf"
          sha256: fb000d39755a008f265dc871bbe3d741e36f97445f385ab99206888f8ac705dd
    pmids:
    homepage:
    mailing_list:
    description: >
      Velour is a memory efficient short read de novo DNA sequence assembly tool for gigabase-scale genomes.