---
version: 0.1.0
images:
  - 
    title: velvet
    image:
      dockerhub: bioboxes/velvet
      repo: https://github.com/bioboxes/velvet
      source: https://github.com/dzerbino/velvet
    pmid: 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.
    tasks:
      - name: default
        interface: assembler
      - name: careful
        interface: assembler
  -
    title: megahit
    image:
      dockerhub: bioboxes/megahit
      repo: https://github.com/bioboxes/megahit
      source: https://github.com/voutcn/megahit
    pmid: 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.
    tasks:
      - name: default
        interface: assembler
      - name: no-mercy
        interface: assembler
  -
    title: idba
    image:
      dockerhub: bioboxes/idba
      repo: https://github.com/bioboxes/idba
      source: https://code.google.com/p/hku-idba/
    pmid: 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.
    tasks:
      - name: default
        interface: assembler
      - name: single-cell
        interface: assembler
      - name: idba
        interface: assembler
  -
    title: soap
    image:
      dockerhub: bioboxes/soap
      repo: https://github.com/bioboxes/soap
      source: http://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/
    pmid: 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.
    tasks:
      - name: default
        interface: assembler
  -
    title: sparse
    image:
      dockerhub: bioboxes/sparse
      repo: https://github.com/bioboxes/sparse
      source: http://sourceforge.net/projects/sparseassembler/
    pmid: 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.
    tasks:
      - name: default
        interface: assembler
      - name: careful
        interface: assembler
  - 
    title: sga
    image:
      dockerhub: bioboxes/sga
      repo: https://github.com/bioboxes/sga
      source: https://github.com/jts/sga
    pmid: 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.
    tasks:
      - name: default
        interface: assembler
      - name: careful
        interface: assembler
  -
    title: minia
    image:
      dockerhub: bioboxes/minia
      repo: https://github.com/rchikhi/docker-minia
      source:
    pmid: 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.
    tasks:
      - name: default
        interface: assembler
  -
    title: ray
    image:
      dockerhub: bioboxes/ray
      repo: https://github.com/sebhtml/ray
      source:
    pmid: 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.
    tasks:
      - name: default
        interface: assembler