BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations
Abstract Background Retroviruses replicate by integrating a DNA copy into a host chromosome. Detecting novel retroviral integrations (ones not in the reference genome sequence of the host) from genomic NGS data is bioinformatically challenging and frequently produces many false positives. One common...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-022-04621-1 |
| _version_ | 1818022226160517120 |
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| author | Emanuele Marchi Mathew Jones Paul Klenerman John Frater Gkikas Magiorkinis Robert Belshaw |
| author_facet | Emanuele Marchi Mathew Jones Paul Klenerman John Frater Gkikas Magiorkinis Robert Belshaw |
| author_sort | Emanuele Marchi |
| collection | DOAJ |
| description | Abstract Background Retroviruses replicate by integrating a DNA copy into a host chromosome. Detecting novel retroviral integrations (ones not in the reference genome sequence of the host) from genomic NGS data is bioinformatically challenging and frequently produces many false positives. One common method of confirmation is visual inspection of an alignment of the chimaeric (split) reads that span a putative novel retroviral integration site. We perceived the need for a program that would facilitate this by producing a multiple alignment containing both the viral and host regions that flank an integration. Results BreakAlign is a Perl program that uses blastn to produce such a multiple alignment. In addition to the NGS dataset and a reference viral sequence, the program requires either (a) the ~ 500nt host genome sequence that spans the putative integration or (b) coordinates of this putative integration in an installed copy of the reference human genome (multiple integrations can be processed automatically). BreakAlign is freely available from https://github.com/marchiem/breakalign and is accompanied by example files allowing a test run. Conclusion 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. |
| first_indexed | 2024-04-14T08:28:33Z |
| format | Article |
| id | doaj.art-f93c3eb8817c4d83a9e60b1652121508 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-14T08:28:33Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-f93c3eb8817c4d83a9e60b16521215082022-12-22T02:03:58ZengBMCBMC Bioinformatics1471-21052022-04-012311810.1186/s12859-022-04621-1BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrationsEmanuele Marchi0Mathew Jones1Paul Klenerman2John Frater3Gkikas Magiorkinis4Robert Belshaw5Nuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordNuffield Department of Medicine, University of OxfordDepartment of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of AthensDepartment of Biology, College of Science and Technology, Wenzhou-Kean UniversityAbstract Background Retroviruses replicate by integrating a DNA copy into a host chromosome. Detecting novel retroviral integrations (ones not in the reference genome sequence of the host) from genomic NGS data is bioinformatically challenging and frequently produces many false positives. One common method of confirmation is visual inspection of an alignment of the chimaeric (split) reads that span a putative novel retroviral integration site. We perceived the need for a program that would facilitate this by producing a multiple alignment containing both the viral and host regions that flank an integration. Results BreakAlign is a Perl program that uses blastn to produce such a multiple alignment. In addition to the NGS dataset and a reference viral sequence, the program requires either (a) the ~ 500nt host genome sequence that spans the putative integration or (b) coordinates of this putative integration in an installed copy of the reference human genome (multiple integrations can be processed automatically). BreakAlign is freely available from https://github.com/marchiem/breakalign and is accompanied by example files allowing a test run. Conclusion 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.https://doi.org/10.1186/s12859-022-04621-1NGSRetrovirusProvirusIntegrationInsertionDetection |
| spellingShingle | Emanuele Marchi Mathew Jones Paul Klenerman John Frater Gkikas Magiorkinis Robert Belshaw BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations BMC Bioinformatics NGS Retrovirus Provirus Integration Insertion Detection |
| title | BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations |
| title_full | BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations |
| title_fullStr | BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations |
| title_full_unstemmed | BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations |
| title_short | BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations |
| title_sort | breakalign a perl program to align chimaeric split genomic ngs reads and allow visual confirmation of novel retroviral integrations |
| topic | NGS Retrovirus Provirus Integration Insertion Detection |
| url | https://doi.org/10.1186/s12859-022-04621-1 |
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