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Casper
Yoann Dufresne edited this page Dec 13, 2018
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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.
- 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.
- 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.
- Casper website: http://best.snu.ac.kr/casper/index.php
- Casper publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-S9-S10