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A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing.

Abstract：

:Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Cantacessi C,Jex AR,Hall RS,Young ND,Campbell BE,Joachim A,Nolan MJ,Abubucker S,Sternberg PW,Ranganathan S,Mitreva M,Gasser RB

doi

10.1093/nar/gkq667

subject

Has Abstract

pub_date

2010-09-01 00:00:00

pages

e171

issue

17

eissn

0305-1048

issn

1362-4962

pii

gkq667

journal_volume

38

pub_type

杂志文章

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