RT Journal Article
SR Electronic
T1 Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 390013
DO 10.1101/390013
A1 Grzegorz M Boratyn
A1 Jean Thierry-Mieg
A1 Danielle Thierry-Mieg
A1 Ben Busby
A1 Thomas L Madden
YR 2018
UL http://biorxiv.org/content/early/2018/08/13/390013.abstract
AB 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. We show that Magic-BLAST is the best at intron discovery over a wide range of conditions. It is versatile and robust to high levels of mismatches or extreme base composition and works well with very long reads. It is reasonably fast. It can align reads to a BLAST database or a FASTA file. It can accept a FASTQ file as input or automatically retrieve an accession from the SRA repository at the NCBI.