Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples
Open Access
- 18 November 2014
- journal article
- method
- Published by Springer Nature in Genome Biology
- Vol. 15 (11) , 1-12
- https://doi.org/10.1186/s13059-014-0519-7
Abstract
We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral genomics studies.Keywords
This publication has 45 references indexed in Scilit:
- Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplificationNucleic Acids Research, 2012
- VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencingGenome Research, 2012
- Synthetic spike-in standards for RNA-seq experimentsGenome Research, 2011
- Full-length transcriptome assembly from RNA-Seq data without a reference genomeNature Biotechnology, 2011
- BamTools: a C++ API and toolkit for analyzing and managing BAM filesBioinformatics, 2011
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing dataGenome Research, 2010
- Architecture and secondary structure of an entire HIV-1 RNA genomeNature, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencingNature Biotechnology, 2009
- Mapping and quantifying mammalian transcriptomes by RNA-SeqNature Methods, 2008