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Yoann Dufresne edited this page Dec 13, 2018 · 5 revisions

This module give you the possibility to get the assembly of the forward and reverse reads.
For space efficiency, the reads are dereplicated after the merging process. A size value is added in each read header to keep the abundance.

Module interactions

Main inputs

  • Forward reads: The FASTQ file containing the forward reads.
  • Reverse reads: The FASTQ file containing the reverse reads.
  • Output file: The FASTQ file within the assembled reads will be outputted.

Options

  • kmer size: Size of the kmers used to align reads.
  • Maximal quality difference: Threshold based on quality score difference between two nucleotides in a mismatch. Under this threshold, the kmer context aware will chose the nucleotide to keep and over the best quality nucleotide.
  • Maximal mismatch ratio: The maximal ratio of mismatches. A 0.5 ratio will allow one base over two.
  • Minimal read length: The minimal length of an assembled read.

References

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