Recent improvements in Magic-BLAST 1.6

We present recent improvements to Magic-BLAST, an RNA-seq mapper that aligns long as well as short reads to target sequences in a BLAST database. The new features include accessing Sequence Read Archive (SRA) reads from cloud buckets, reporting National Center for Biotechnology Information (NCBI) taxonomy ID's, and reporting unaligned reads in a separate file. A powerful Magic-BLAST feature is that it can access reads from SRA by accession, making pipelines with Magic-BLAST more reusable. NCBI hosts SRA data at cloud providers, supporting large scale hyper-parallel data analyses. Magic-BLAST 1.6.0 downloads SRA data from the cloud. Benefits include uninterrupted downloads, faster download speeds, and huge bandwidth for parallel downloads to multiple running processes or cloud instances. Magic-BLAST provides NCBI taxonomy ID's in the SAM report. Using taxonomy ID's allows unambiguous mapping to taxonomic nodes. This is especially useful for metagenomic projects. Magic-BLAST can report unaligned reads in a separate file in SAM, tabular, or FASTA formats. In this fashion Magic-BLAST can, for example, be used as for contamination screening or for separating virus and host reads from a next-generation sequencing run. This research was supported by the Intramural Research Program of the National Library of Medicine at the NIH.