Casper

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

• Casper website: http://best.snu.ac.kr/casper/index.php
• Casper publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-S9-S10