PerM

Software Summary

Mesabi

Default Module: 
Other Modules Available: 
Last Updated On: 

Itasca

Default Module: 
Other Modules Available: 
Last Updated On: 

Lab

Default Module: 

4.0

Other Versions Available: 

4.0

Last Updated On: 

Wednesday, December 7, 2016

Last Updated On: 

Wednesday, December 7, 2016

Support Level: 
Minimal Support
Software Access Level: 
Open Access
Software Categories: 
Genetics
Software Description
Software Description: 

PerM is 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. Today PerM is capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.

 

Algorithm and Performance:

 

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 43 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.

 

Additional Information

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