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Bioinformatics (2011) 27(4), 1915–1921.
The authors find it worth mentioning that the parameters used to run the PerM mapper were not optimal to achieve full sensitivity. Based on the new recommendations of the developers of PerM, we used the latest version of PerM (v. 0.3.6), and updated two parameters as follows:
Previously, we have used ‘–seed S20 -k 10000 -v 4’. With this update, PerM now achieves full sensitivity in our simulation experiment. With real datasets (Table 6), PerM tends to map more reads compared with Bowtie, but maps slightly less than Mapreads and SOCS.