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  • Soap De Novo assembly interpretation

    Hello!

    I have run soap de novo on my assembly, and I have used different kmers. I have 12 assemblies and I need to choose the best one out of those 12.
    There are around 21 files created in each of the 12 assemblies.
    My question is, how should I interpret these files so as to choose the best assembly (things like n50, contig size-max,min; no. of contigs, coverage, assembly size etc).
    Which files should I use to get these results?
    The 21 files are:
    .arc
    .contig
    .contigIndex
    .edge
    .updated.edge
    .gapSeq
    .kmerFreq
    .links
    .markonEdge
    .newContigIndex
    .path
    .peGrads
    .preArc
    .preGraphBasic
    .readInGap
    .readOnContig
    .scaf
    .scaf_gap
    .scafSeq
    .vertex

    Thanks so much for the help!!

  • #2
    I worked on SOAP assemblies a while ago and I think .scafseq is the fasta file of the scaffolded sequences and you'd likely be evaluating the contiguity metrics of your assemblies on this one. I can't remember the name for the contig fasta file.

    Comment


    • #3
      A file called .scafStatistics should have the basic information on N50, total size of assembly etc.

      Comment

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