bioRxiv preprint doi: https://doi.org/10.1101/390013; this version posted August 13, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads Grzegorz M Boratyn, Jean Thierry-Mieg*, Danielle Thierry-Mieg, Ben Busby and Thomas L Madden* National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA * To whom correspondence should be addressed. Tel: 301-435-5987; Fax: 301-480-4023; Email:
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[email protected]. ABSTRACT Next-generation sequencing technologies can produce tens of millions of reads, often paired-end, from transcripts or genomes. But few programs can align RNA on the genome and accurately discover introns, especially with long reads. To address these issues, we introduce Magic-BLAST, a new aligner based on ideas from the Magic pipeline. It uses innovative techniques that include the optimization of a spliced alignment score and selective masking during seed selection. We evaluate the performance of Magic-BLAST to accurately map short or long sequences and its ability to discover introns on real RNA-seq data sets from PacBio, Roche and Illumina runs, and on six benchmarks, and compare it to other popular aligners. Additionally, we look at alignments of human idealized RefSeq mRNA sequences perfectly matching the genome.