<![CDATA[BOL: Reference-free prediction of rearrangement breakpoint reads]]> https://bioinformaticsonline.com/bookmarks/view/35899/reference-free-prediction-of-rearrangement-breakpoint-reads? https://bioinformaticsonline.com/bookmarks/view/35899/reference-free-prediction-of-rearrangement-breakpoint-reads Thu, 08 Mar 2018 05:05:25 -0600 https://bioinformaticsonline.com/bookmarks/view/35899/reference-free-prediction-of-rearrangement-breakpoint-reads <![CDATA[Reference-free prediction of rearrangement breakpoint reads]]> lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing depth of 100×, it finds ∼88% of the breakpoints correctly with no false-positive reads. Moreover, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion transcripts correctly than previous approaches, and yet produces fewer false-positive reads. To our knowledge, this is the first method to detect breakpoint reads without using a reference genome.

https://github.com/ewijaya/slidesort-bpr

Address of the bookmark: https://code.google.com/archive/p/slidesort-bpr/

]]> Neel