Introduction

MOTIVATION: Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed. RESULTS: We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets. AVAILABILITY: Xenome is available for non-commercial use from http://www.nicta.com.au/bioinformatics.

Publications

  1. Xenome--a tool for classifying reads from xenograft samples.
    Cite this
    Conway T, Wazny J, Bromage A, Tymms M, Sooraj D, Williams ED, Beresford-Smith B, 2012-06-01 - Bioinformatics (Oxford, England)

Credits

  1. Thomas Conway
    Developer

  2. Jeremy Wazny
    Developer

  3. Andrew Bromage
    Developer

  4. Martin Tymms
    Developer

  5. Dhanya Sooraj
    Developer

  6. Elizabeth D Williams
    Developer

  7. Bryan Beresford-Smith
    Investigator

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Summary
AccessionBT006358
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByBryan Beresford-Smith