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ISMB/ECCB
TT05: Hannes Ponstingl - The SSAHA2 software pipeline for the mapping of DNA sequencing reads and genotype calling
Originally for alignment of capillary sequencing, modified to handle short read data. Uses k-mer hashed genome and Smith-Waterman. Can handle paired end reads. Accurately maps a high percentage of reads on simulated data. Has pipeline for calling SNPs, indels - also tested on simulated data. I/O is all text based. Outputs FASTQ, CIGAR, SAM. Can pre-calculate genome hash and can be tuned to run with relatively limited memory requirements. Free to use. - Cass Johnston
question: parallelization? Yes. - Cass Johnston
question: source code availability? Some of the code is from phrap and is proprietary so no. Binaries free to download though - Cass Johnston