Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler.

ABSTRACT:

Background

Deep sequencing makes it possible to observe low-frequency viral variants and sub-populations with greater accuracy and sensitivity than ever before. Existing platforms can be used to multiplex a large number of samples; however, analysis of the resulting data is complex and involves separating barcoded samples and various read manipulation processes ending in final assembly. Many assembly tools were designed with larger genomes and higher fidelity polymerases in mind and do not perform well with reads derived from highly variable viral genomes. Reference-based assemblers may leave gaps in viral assemblies while de novo assemblers may struggle to assemble unique genomes.

Results

The IRMA (iterative refinement meta-assembler) pipeline solves the problem of viral va

SUBMITTER: Shepard SS 

PROVIDER: S-EPMC5011931 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature