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Periodic Seed Mapping PerM

Provides highly efficient mapping solutions for genome-scale mapping projects involving Illumina or SOLiD data. The data structure in PerM requires only 4.5 bytes per base to index the human genome, allowing entire genomes to be loaded to memory, while multiple processors simultaneously map reads to the reference. PerM owes its performance primarily to the use of single periodic spaced seeds which are capable of providing sufficient weight and sensitivity to significantly increase genome-scale mapping performance in comparison with other mapping programs.

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PerM classification

PerM specifications

Software type:
Restrictions to use:
Biological technology:
Illumina, Life Technologies
Apache License version 2.0
Command line interface
Input data:
A reference sequence, a read as the input files.
Operating system:
Computer skills:

PerM distribution


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PerM support



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Program in Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA, USA

Funding source(s)

National Institutes of Health Center of Excellence in Genomic Sciences

Link to literature

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