Magic-BLAST, an accurate DNA and RNA-seq mapper for long and short reads

Authors

• GM Boratyn
• J Thierry-Mieg
• D Thierry-Mieg
• TL Madden

Abstract

Next-generation sequencing (NGS) technologies facilitate rapid analysis of gene expression across individuals, tissues, or conditions. Mapping reads against a reference genome is the first step in many genomics analysis pipelines. It is therefore essential to map the reads reliably. Many algorithms were developed to tackle this problem however few of them can map long reads well. We present Magic-BLAST, a new NCBI tool for mapping NGS runs against a genome or transcriptome. It incorporates ideas from the MAGIC-AceView pipeline implemented within BLAST code base. Magic-BLAST is very robust across wide range of conditions. It works well with reads generated by Illumina, Roche 454, and PacBio platforms. It also provides very good performance when mapping against genomes with biased compositions or from related species. We evaluated performance of Magic-BLAST to accurately map reads and discover introns on real and simulated RNA-seq data and compared it with popular programs: Hisat2, STAR, and TopHat2. Magic-BLAST provides the best performance in intron discovery. Magic-BLAST is convenient to use. It does not need any special tuning for different technologies and genomes. It works well in different conditions using default parameters. It directly accesses reads stored in the NCBI Sequence Read Archive (SRA), without the need to download the data beforehand, works with BLAST databases, and integrates well with NCBI facilities and services.

Scientific Focus Area: Computational Biology

This page was last updated on Friday, March 26, 2021