Platform for Drug Discovery


SOAPdenovo scaf and GapCloser (PE)


Introduction


    This pipeline first orients the initial assembly contigs using mate-pair sequences to create a scaffold sequences. Next, remaps raw sequence reads to the scaffold sequences to fill the gaps in scaffolds, improving the assembly quality.


    Input formatFASTQ, FASTA
    Library layoutPaired-end
    SpeciesUnspecified
    Execution timeAbout 1 hour. (7M paired-end reads[50bp+50bp])

Inputs


    Raw NGS reads (FASTQ format, Paired-end): 1-10


    Genome assembly (Contig or Scaffold sequences) (FASTA format): 1


Outputs


    Workflow

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    SOAPdenovo statistics

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    Gap-filled scaffold sequences

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Comments


    Caution: SOAPdenovo replaces N with G in input FASTA file in order to filter ambiguous bases.

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