PerM

Description

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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. Template:App Location

Available versions

• 0.3.6 (EL5)
• 0.4.0 (EL6)

Running the application using modules

To use perm with the environment modules system at HPC the following commands are available:

Get module information for perm:

$module spider perm

Load the default application module:

$module load perm

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_PERM_DIR - directory where perm is located.

How To Run

The reference sequence(s) can be whole genomes with multiple chromosomes, the transcriptome or even the millions reads in the fasta format, separated by '>'. The reads can be in the fasta, fastq, csfasta + QUAL formats or fastq for SOLiD reads. PerM can output alignments in our mapping format or the SAM format and that output can be further processed by ComB, SAMtools, RseqFlow pipeline and the Galaxy. Check the manual for more detail.

Two binaries are available - PerM and PerM-OMP (OpenMP multi-threaded version).