![]() SNAP has one additional utility, the SNAPCommand program which sends alignment jobs to SNAP when it is running in daemon mode. In addition, you can download binaries for Windows, Linux and OSX: SNAP is available under an Apache 2 license at /amplab/snap. SNAP was developed by a team from Microsoft Research, the UC Berkeley AMP Lab, and UCSF. SNAP does all of these tasks in a single tool, and is usually more than 10x faster than the standard samtools/Picard pipeline. Other aligners produce unsorted SAM (or in the case of Novoalign unsorted BAM) output, and require the use of other tools to compress, sort, mark duplicates and index the final output file. In addition to taking FASTQ (unprocessed reads) as input, it also accepts SAM and BAM (aligned reads). SNAP is also more full-featured than other aligners. When used with Haplotype Caller from the Genome Analysis Toolkit, SNAP produces better concordance with known-truth sets than other aligners for most of the genome-in-a-bottle and Illumina Platinum genomes. SNAP is from 2-5x faster than commonly used aligners like BWA-mem2 and Bowtie2, and 20x-nearly 30x faster than Novoalign. This is a computationally challenging problem because reference genomes are big (the human genome is over 3 billion base pairs long) and are often highly repetitive. It takes data from gene sequencing hardware that consists of short chunks of DNA (typically 70-300 base pairs long) called reads and determines where, how well and how unambiguously they match to a given reference genome. SNAP is a program that is part of a gene sequencing pipeline.
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