منابع مشابه
PyBamView: a browser-based application for viewing short read alignments
UNLABELLED Current sequence alignment browsers allow visualization of large and complex next-generation sequencing datasets. However, most of these tools provide inadequate display of insertions and can be cumbersome to use on large datasets. I implemented PyBamView, a lightweight Web application for visualizing short read alignments. It provides an easy-to-use Web interface for viewing alignme...
متن کاملPOPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments
BACKGROUND While many bioinformatics tools currently exist for assembling and discovering variants from next-generation sequence data, there are very few tools available for performing evolutionary analyses from these data. Evolutionary and population genomics studies hold great promise for providing valuable insights into natural selection, the effect of mutations on phenotypes, and the origin...
متن کاملClustering of Short Read Sequences for de novo Transcriptome Assembly
Given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. In this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. First, the contiguous sequencesare generated using de Bruijn graph with d...
متن کاملBamView: visualizing and interpretation of next-generation sequencing read alignments
UNLABELLED 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 t...
متن کاملSashimi plots: Quantitative visualization of RNA sequencing read alignments
We introduce Sashimi plots, a quantitative multi-sample visualization of mRNA sequencing reads aligned to gene annotations. Sashimi plots are made using alignments (stored in the SAM/BAM format) and gene model annotations (in GFF format), which can be custom-made by the user or obtained from databases such as Ensembl or UCSC. We describe two implementations of Sashimi plots: (1) a stand-alone c...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2013
ISSN: 1471-2105
DOI: 10.1186/1471-2105-14-s11-s4