NSIT: Novel Sequence Identification Tool
<p dir="ltr">Novel sequences are DNA sequences present in an individual's genome but absent in the human reference assembly. They are predicted to be biologically important, both individual and population specific, and consistent with the known human migration paths. Recent work...
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2014
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| _version_ | 1864513506676572160 |
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| author | Benjarath Pupacdi (635765) |
| author2 | Asif Javed (236620) Mohammed J. Zaki (257966) Mathuros Ruchirawat (272859) |
| author2_role | author author author |
| author_facet | Benjarath Pupacdi (635765) Asif Javed (236620) Mohammed J. Zaki (257966) Mathuros Ruchirawat (272859) |
| author_role | author |
| dc.creator.none.fl_str_mv | Benjarath Pupacdi (635765) Asif Javed (236620) Mohammed J. Zaki (257966) Mathuros Ruchirawat (272859) |
| dc.date.none.fl_str_mv | 2014-09-29T06:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pone.0108011 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/NSIT_Novel_Sequence_Identification_Tool/26860975 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Bioinformatics and computational biology Genetics Biomedical and clinical sciences Clinical sciences Sequence alignment Human genomics Chromosomes Mammalian genomics Chromosome mapping Computer software Epstein-Barr virus Zebrafish |
| dc.title.none.fl_str_mv | NSIT: Novel Sequence Identification Tool |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">Novel sequences are DNA sequences present in an individual's genome but absent in the human reference assembly. They are predicted to be biologically important, both individual and population specific, and consistent with the known human migration paths. Recent works have shown that an average person harbors 2–5 Mb of such sequences and estimated that the human pan-genome contains as high as 19–40 Mb of novel sequences. To identify them in a de novo genome assembly, some existing sequence aligners have been used but no computational method has been specifically proposed for this task. In this work, we developed <b>NSIT</b> (<b>N</b>ovel <b>S</b>equence <b>I</b>dentification <b>T</b>ool), a software that can accurately and efficiently identify novel sequences in an individual's de novo whole genome assembly. We identified and characterized 1.1 Mb, 1.2 Mb, and 1.0 Mb of novel sequences in NA18507 (African), YH (Asian), and NA12878 (European) de novo genome assemblies, respectively. Our results show very high concordance with the previous work using the respective reference assembly. In addition, our results using the latest human reference assembly suggest that the amount of novel sequences per individual may not be as high as previously reported. We additionally developed a graphical viewer for comparisons of novel sequence contents. The viewer also helped in identifying sequence contamination; we found 130 kb of Epstein-Barr virus sequence in the previously published NA18507 novel sequences as well as 287 kb of zebrafish repeats in NA12878 de novo assembly. NSIT requires2GB of RAM and 1.5–2 hrs on a commodity desktop. The program is applicable to input assemblies with varying contig/scaffold sizes, ranging from 100 bp to as high as 50 Mb. It works in both 32-bit and 64-bit systems and outperforms, by large margins, other fast sequence aligners previously applied to this task. To our knowledge, NSIT is the first software designed specifically for novel sequence identification in a de novo human genome assembly.</p><h2>Other Information</h2><p dir="ltr">Published in: PLOS ONE<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1371/journal.pone.0108011" rel="noreferrer" target="_blank">https://dx.doi.org/10.1371/journal.pone.0108011</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_092208a44d9961492975741a9a2b8956 |
| identifier_str_mv | 10.1371/journal.pone.0108011 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/26860975 |
| publishDate | 2014 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | NSIT: Novel Sequence Identification ToolBenjarath Pupacdi (635765)Asif Javed (236620)Mohammed J. Zaki (257966)Mathuros Ruchirawat (272859)Biological sciencesBioinformatics and computational biologyGeneticsBiomedical and clinical sciencesClinical sciencesSequence alignmentHuman genomicsChromosomesMammalian genomicsChromosome mappingComputer softwareEpstein-Barr virusZebrafish<p dir="ltr">Novel sequences are DNA sequences present in an individual's genome but absent in the human reference assembly. They are predicted to be biologically important, both individual and population specific, and consistent with the known human migration paths. Recent works have shown that an average person harbors 2–5 Mb of such sequences and estimated that the human pan-genome contains as high as 19–40 Mb of novel sequences. To identify them in a de novo genome assembly, some existing sequence aligners have been used but no computational method has been specifically proposed for this task. In this work, we developed <b>NSIT</b> (<b>N</b>ovel <b>S</b>equence <b>I</b>dentification <b>T</b>ool), a software that can accurately and efficiently identify novel sequences in an individual's de novo whole genome assembly. We identified and characterized 1.1 Mb, 1.2 Mb, and 1.0 Mb of novel sequences in NA18507 (African), YH (Asian), and NA12878 (European) de novo genome assemblies, respectively. Our results show very high concordance with the previous work using the respective reference assembly. In addition, our results using the latest human reference assembly suggest that the amount of novel sequences per individual may not be as high as previously reported. We additionally developed a graphical viewer for comparisons of novel sequence contents. The viewer also helped in identifying sequence contamination; we found 130 kb of Epstein-Barr virus sequence in the previously published NA18507 novel sequences as well as 287 kb of zebrafish repeats in NA12878 de novo assembly. NSIT requires2GB of RAM and 1.5–2 hrs on a commodity desktop. The program is applicable to input assemblies with varying contig/scaffold sizes, ranging from 100 bp to as high as 50 Mb. It works in both 32-bit and 64-bit systems and outperforms, by large margins, other fast sequence aligners previously applied to this task. To our knowledge, NSIT is the first software designed specifically for novel sequence identification in a de novo human genome assembly.</p><h2>Other Information</h2><p dir="ltr">Published in: PLOS ONE<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1371/journal.pone.0108011" rel="noreferrer" target="_blank">https://dx.doi.org/10.1371/journal.pone.0108011</a></p>2014-09-29T06:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1371/journal.pone.0108011https://figshare.com/articles/journal_contribution/NSIT_Novel_Sequence_Identification_Tool/26860975CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/268609752014-09-29T06:00:00Z |
| spellingShingle | NSIT: Novel Sequence Identification Tool Benjarath Pupacdi (635765) Biological sciences Bioinformatics and computational biology Genetics Biomedical and clinical sciences Clinical sciences Sequence alignment Human genomics Chromosomes Mammalian genomics Chromosome mapping Computer software Epstein-Barr virus Zebrafish |
| status_str | publishedVersion |
| title | NSIT: Novel Sequence Identification Tool |
| title_full | NSIT: Novel Sequence Identification Tool |
| title_fullStr | NSIT: Novel Sequence Identification Tool |
| title_full_unstemmed | NSIT: Novel Sequence Identification Tool |
| title_short | NSIT: Novel Sequence Identification Tool |
| title_sort | NSIT: Novel Sequence Identification Tool |
| topic | Biological sciences Bioinformatics and computational biology Genetics Biomedical and clinical sciences Clinical sciences Sequence alignment Human genomics Chromosomes Mammalian genomics Chromosome mapping Computer software Epstein-Barr virus Zebrafish |