Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.

parsing SAM files to extract chimeric alignments and report each chimeric locus with its supporting reads

A python script that implements an efficient algorithm for the Chimeric Alignment problem. A virus infects a bacterium and modifies a replication process in the bacterium by adding for each A an A sequence of length 1-5, for each C a C sequence of length 1-10, for each G a G sequence of length >= 1 and for each T a T sequence of length >= 1.