alkanlab/mrfast repository overview

mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respect to the library settings. mrFAST is designed to find 'all' mappings for a given set of reads, however it can return one "best" map location if the relevant parameter is invoked.

Refer to mrFAST wiki for details: https://github.com/BilkentCompGen/mrfast/wiki⁠

NOTE: mrFAST is developed for Illumina, thus requires all reads to be at the same length. For paired-end reads, lengths of mates may be different from each other, but each "side" should have a uniform length.

Sample Docker-based command line assuming the working directory is /home/mrfast/samplerun:

docker run --user=$UID -v /home/mrfast/samplerun/:/input -v /home/mrfast/samplerun:/output mrfast --search /input/human_g1k_v37.fasta --seq1 /input/f1.fastq --seq2 /input/f2.fastq --pe --min 0 --max 1000 -o /output/test.sam