BreakAlign

BreakAlign aligns chimaeric (split) genomic next-generation sequencing reads to detect and help confirm novel retroviral integrations within host genomes.

Key Features:

• Implementation: Implemented in Perl.
• Multiple alignment generation: Uses the BLASTN algorithm to produce multiple alignments that include viral sequence and adjacent host genomic regions flanking a suspected integration site for confirmation and visual inspection.
• Input requirements: Accepts approximately 500 nucleotides of host genome sequence spanning the putative integration or coordinates of the integration within an installed reference human genome.
• Sequencing data compatibility: Applicable to short-read next-generation sequencing (NGS) data and long-read (third generation) sequencing data.
• Mobile element support: Can be used with any mobile element that has at least one conserved flanking region.
• Application focus: Aids identification and reduction of false positives in bioinformatic detection of novel retroviral integrations.

Scientific Applications:

• Integration discovery and validation: Detection and confirmation of novel retroviral integration sites from chimaeric sequencing reads.
• Germline integration characterization: Characterization of endogenous retrovirus germline integrations within host genomes.
• Somatic integration characterization: Characterization of somatic integrations of exogenous retroviruses, including HIV and HTLV.
• Cross-platform integration mapping: Mapping mobile element integrations across short-read and long-read sequencing datasets when conserved flanking regions are present.

Methodology:

Implemented in Perl and using BLASTN to generate multiple alignments that include viral and adjacent host genomic regions flanking putative integration sites, requiring ~500 nt of host sequence or coordinates in an installed reference human genome, and applicable to short-read NGS and long-read (third-generation) sequencing and mobile elements with conserved flanking regions.