Sentence examples for mapping parameters were from inspiring English sources
For the first analyzed short read library (accession SRX759525), mapping parameters were set to a local alignment ("--very-fast-local") with multi-mapping allowed (value k = 10).
High stringency mapping parameters were used, which allowed for a maximum of 2 mismatches.
Relatively loose mapping parameters were chosen to reduce the probability of false positive low-coverage regions.
Mapping parameters were adjusted to map a maximum number of reads to the reference bacterial genomes.
Our standard mapping parameters were set to allow six mismatches per 50 nt-read alignment.
The following mapping parameters were employed (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.5, similarity: 0.8).
Furthermore, because the present algorithm is derived from a physiological model of HVS, the meanings of tone mapping parameters are clear as in Section 2.3.
Hence, if the mapping parameters are too stringent some of the reads may not be mapped.
The choice of the exact mapping parameters is highly dependent on the polymorphism pattern and levels in the target organism.
Advice on mapping parameters is included in the documentation.
In order to eliminate these matches, stringency of read mapping parameters was increased.
