Interpreting Viral Deep Sequencing Data with GLUE.

ABSTRACT: Using deep sequencing technologies such as Illumina's platform, it is possible to obtain reads from the viral RNA population revealing the viral genome diversity within a single host. A range of software tools and pipelines can transform raw deep sequencing reads into Sequence Alignment Mapping (SAM) files. We propose that interpretation tools should process these SAM files, directly translating individual reads to amino acids in order to extract statistics of interest such as the proportion of different amino acid residues at specific sites. This preserves per-read linkage between nucleotide variants at different positions within a codon location. The samReporter is a subsystem of the GLUE software toolkit which follows this direct read translation approach in its processing of SAM files.

SUBMITTER: Singer JB 

PROVIDER: S-EPMC6520954 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature