Both paired end whole transcriptome shotgun sequencing (RNA-Seq), and paired end Whole Genome Shotgun Sequencing (WGSS), can be used to discover rearrangements in tumour genomes. Comrad leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as expressed or not expressed and accurate classification of the genomic or non-genomic origin of aberrant transcripts. A major benefit of Comrad is its ability to accurately identify aberrant transcripts and associated rearrangements using low coverage genome data.

Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data

McPherson A, Wu C, Hajirasouliha I, Hormozdiari Fe, Hach F, Lapuk AV, Volik S, Shah SP, Collins CC, Sahinalp SC

Bioinformatics (2011) 27 (11): 1481-1488
Presented at ISMB-HitSeq’11 (High Throughput Sequencing Analysis and Algorithms, Special Interest Group of ISMB’11), Vienna, Austria, July 15-16 2011
Journal link | PubMed ID: 21478487 |