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A software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms.

Software type:
Command line interface
Restrictions to use:
Biological technology:
Illumina, Life Technologies
Operating system:
Apache License version 2.0
Computer skills:
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  • (Chen et al., 2009) PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics.
    PMID: 19675096
  • (Fonseca et al., 2012) Tools for mapping high-throughput sequencing data. Bioinformatics.
    PMID: 23060614
  • (Li and Homer, 2010) A survey of sequence alignment algorithms for next-generation sequencing. Briefings in bioinformatics.
    PMID: 20460430
  • (Ruffalo et al., 2011) Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics.
    PMID: 21856737
  • (Hatem et al., 2013) Benchmarking short sequence mapping tools. BMC bioinformatics.
    PMID: 23758764

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