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IDBA-MT: De novo Assembler for Metatranscriptomic Data generated from Next-Generating Sequencing Technology
| Citations: | 2 - 1 self |
BibTeX
@MISC{Leung_idba-mt:de,
author = {Henry C. M. Leung and S. M. Yiu and John Parkinson and Francis Y. L. Chin},
title = {IDBA-MT: De novo Assembler for Metatranscriptomic Data generated from Next-Generating Sequencing Technology},
year = {}
}
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Abstract
Motivation: High-throughput next-generation sequencing technology provides a great opportunity for analyzing metatranscriptomic data. However, the reads produced by these technologies are short and an assembling step is required to combine the short reads into longer contigs. As there are many repeat patterns in mRNAs from different genomes and the abundance ratio of mRNAs in a sample varies a lot, existing assemblers for genomic data, transcriptomic data and metagenomic data do not work on metatranscriptomic data and produce chimeric contigs, i.e. incorrect contigs formed by merging multiple mRNA sequences. To our best knowledge, there is no assembler designed for metatranscriptomic data. Results: In this paper, we introduced an assembler called IDBA-MT which is designed for assembling reads from metatranscriptomic data. Compared with other assemblers, IDBA-MT produces much fewer chimeric contigs (reduce by 50 % or more) when compared with existing assemblers like Oases, IDBA-UD and Trinity. 1
Keyphrases
metatranscriptomic data next-generating sequencing technology chimeric contigs short read transcriptomic data high-throughput next-generation multiple mrna sequence assembling step abundance ratio different genome incorrect contigs metagenomic data many repeat pattern genomic data great opportunity
