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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.

Required Modules

modules documentation


  • perm

System Variables

  • HPC_PERM_DIR - installation directory

Additional Information

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).


  • Validated 4/5/2018