Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments.

Tópicos

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Resumo

LABELLED: So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have been aligned to a reference sequence. It is a desktop application for browsing the aligned or mapped reads [Ruffalo, M, LaFramboise, T, Koyut?rk, M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011;27:2790-6] at different levels of magnification, from nucleotide level, where the base qualities can be seen, to genome or chromosome level where overall coverage is shown. To enable in-depth investigation of NGS data, various views are provided that can be configured to highlight interesting aspects of the data. Multiple read alignment files can be overlaid to compare results from different experiments, and filters can be applied to facilitate the interpretation of the aligned reads. As well as being a standalone application it can be used as an integrated part of the Artemis genome browser, BamView allows the user to study NGS data in the context of the sequence and annotation of the reference genome. Single nucleotide polymorphism (SNP) density and candidate SNP sites can be highlighted and investigated, and read-pair information can be used to discover large structural insertions and deletions. The application will also calculate simple analyses of the read mapping, including reporting the read counts and reads per kilobase per million mapped reads (RPKM) for genes selected by the user.AVAILABILITY: BamView and Artemis are freely available software. These can be downloaded from their home pages: http://bamview.sourceforge.net/; http://www.sanger.ac.uk/resources/software/artemis/. Requirements: Java 1.6 or higher.

Resumo Limpo

label socal nextgener sequenc ngs provid abil sequenc massiv scale low cost enabl biologist perform power experi gain insight biolog process bamview develop visual analys sequenc read ngs platform align refer sequenc desktop applic brows align map read ruffalo m laframbois t koyutrk m compar analysi algorithm nextgener sequenc read align bioinformat differ level magnif nucleotid level base qualiti can seen genom chromosom level overal coverag shown enabl indepth investig ngs data various view provid can configur highlight interest aspect data multipl read align file can overlaid compar result differ experi filter can appli facilit interpret align read well standalon applic can use integr part artemi genom browser bamview allow user studi ngs data context sequenc annot refer genom singl nucleotid polymorph snp densiti candid snp site can highlight investig readpair inform can use discov larg structur insert delet applic will also calcul simpl analys read map includ report read count read per kilobas per million map read rpkm gene select useravail bamview artemi freeli avail softwar can download home page httpbamviewsourceforgenet httpwwwsangeracukresourcessoftwareartemi requir java higher

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