PerM
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Application data |
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| Created by | Yangho Chen, Tade Souaiaia, Ting Chen* |
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| Biological application domain(s) | Genomics, SNP detection |
| Principal bioinformatics method(s) | Read mapping |
| Technology | Illumina, ABI SOLiD |
| Created at | University of Southern California |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ |
| Programming language(s) | C++ |
| Licence | Apache License 2.0 |
| Operating system(s) | Linux |
Summary: PerM (Periodic Seed Mapping) uses periodic spaced seeds to significantly improve mapping efficiency for large reference genomes when compared to state-of-the-art programs.
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Description
With its special periodic spaced seeds, PerM can be fully sensitive to four mismatches, and highly sensitive to higher numbers of mismatches. This seed matching method has speed advantages in longer read (although limited to 64bp currently), non-mappable reads (for fixed number of shift and checking) and in the genome scale mapping due to the high seed weight. PerM is about 37 million reads per CPU hour, full sensitive to 3 mismatches and highly sensitive to more than 3 mismatches for 50bp SOLiD reads. PerM can build the reference index in parallel; it takes half hour to build the human genome index with 16 CPUs and 15 GB memory.
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References
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