BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations.

Emanuele MarchiMathew JonesPaul KlenermanJohn FraterGkikas MagiorkinisRobert D Belshaw

Published in: BMC bioinformatics (2022)

BreakAlign will confirm and facilitate characterisation of both (a) germline integrations of endogenous retroviruses and (b) somatic integrations of exogenous retroviruses such as HIV and HTLV. Although developed for use with genomic short-read NGS (second generation) data and retroviruses, it should also be useful for long-read (third generation) data and any mobile element with at least one conserved flanking region.

Keyphrases

copy number
electronic health record
single molecule
big data
antiretroviral therapy
hiv infected
hepatitis c virus
human immunodeficiency virus
hiv positive
quality improvement
transcription factor
hiv aids
hiv testing
dna repair
gene expression
machine learning