Anyone have philosophical objections to swapping in or adding Spades as an assembler?

[DCGenomics]

No description provided.

[pcantalupo]

Not me. Go for it 👍

As a side note, I tried to install several different assemblers during the March '17 hackathon. Here are my raw notes:

• Metavelvet - too many dependencies
• metaSpades - no because input must be paired end
• IDBA - problems with compiling on MacOSX clang: error: unsupported option '-fopenmp' ppwwyyxx/OpenPano#16.
  • Also getting error when trying to use their Docker image
    • docker run -v pwd:/data -w /data loneknightpy/idba idba_ud -r read.fa -o output
      • terminate called after throwing an instance of 'std::logic_error'
      • what(): SequenceReader::SequenceReader() istream is invalid
• SoapDenovo2 - compile problems: ld: symbol(s) not found for architecture x86_64