Magic-BLAST, an accurate RNA-seq aligner for long and short reads.

ABSTRACT:

Background

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. We introduce Magic-BLAST, a new aligner based on ideas from the Magic pipeline.

Results

Magic-BLAST 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

SUBMITTER: Boratyn GM 

PROVIDER: S-EPMC6659269 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature