Nautilus: a bioinformatics package for the analysis of HIV type 1 targeted deep sequencing data.
作者： Gustavo H. Kijak , Phuc Pham , Eric Sanders-Buell , Elizabeth A. Harbolick , Leigh Anne Eller
关键词: Viral quasispecies 、 Scripting language 、 Java 、 Python (programming language) 、 Biology 、 Bioinformatics 、 Context (language use) 、 DNA sequencing 、 Deep sequencing 、 OS X
摘要: The advent of next generation sequencing technologies is providing new insight into HIV-1 diversity and evolution, which has created the need for bioinformatics tools that could be applied to characterization viral quasispecies. Here we present Nautilus, a package analysis targeted deep data. DeepHaplo module determines nucleotide base frequency read depth at each position computes haplotype frequencies based on linkage among polymorphisms in same sequence read. Motifs variants setting their context mapping orientation, allows validation haplotypes when strand bias suspected. Both modules are accessed through user-friendly GUI, runs Mac OS X (version 10.7.4 or later), Python, JAVA, R scripts. Nautilus available from www.hivresearch.org/research.php?ServiceID=5&SubServiceID=6.
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