Long-read mapping to repetitive reference sequences using Winnowmap2.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
06 2022
06 2022
Historique:
received:
22
05
2021
accepted:
17
03
2022
pubmed:
3
4
2022
medline:
14
6
2022
entrez:
2
4
2022
Statut:
ppublish
Résumé
Approximately 5-10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often yield incorrect alignments and variant calls within long, near-identical repeats, as they remain vulnerable to allelic bias. In the presence of a nonreference allele within a repeat, a read sampled from that region could be mapped to an incorrect repeat copy. To address this limitation, we developed a new long-read mapping method, Winnowmap2, by using minimal confidently alignable substrings. Winnowmap2 computes each read mapping through a collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats. Our experiments highlight that Winnowmap2 successfully addresses the issue of allelic bias, enabling more accurate downstream variant calls in repetitive sequences.
Identifiants
pubmed: 35365778
doi: 10.1038/s41592-022-01457-8
pii: 10.1038/s41592-022-01457-8
pmc: PMC10510034
mid: NIHMS1928677
doi:
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
705-710Subventions
Organisme : Intramural NIH HHS
ID : Z99 HG999999
Pays : United States
Organisme : Intramural NIH HHS
ID : ZIA HG200398
Pays : United States
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
Nat Biotechnol. 2020 Nov;38(11):1309-1316
pubmed: 32665660
Nat Methods. 2022 Jun;19(6):687-695
pubmed: 35361931
Cell. 2019 Jan 24;176(3):663-675.e19
pubmed: 30661756
Bioinformatics. 2019 Jan 1;35(1):20-27
pubmed: 30561550
Gigascience. 2017 Apr 1;6(4):1-6
pubmed: 28327957
Nat Biotechnol. 2019 Oct;37(10):1155-1162
pubmed: 31406327
Bioinformatics. 2018 Sep 1;34(17):i748-i756
pubmed: 30423094
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095
G3 (Bethesda). 2015 Mar 17;5(5):931-41
pubmed: 25787242
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Bioinformatics. 2004 Dec 12;20(18):3363-9
pubmed: 15256412
Genome Res. 2017 May;27(5):747-756
pubmed: 28320918
Genome Res. 2020 Sep;30(9):1291-1305
pubmed: 32801147
Nature. 2021 May;593(7857):101-107
pubmed: 33828295
Nat Biotechnol. 2020 Nov;38(11):1347-1355
pubmed: 32541955
Nat Methods. 2018 Jun;15(6):461-468
pubmed: 29713083
Bioinformatics. 2017 Oct 01;33(19):3088-3090
pubmed: 28575171
Bioinformatics. 2013 Jan 1;29(1):119-21
pubmed: 23129296
Nat Genet. 2015 Jun;47(6):682-8
pubmed: 25915597
Genome Res. 2017 May;27(5):665-676
pubmed: 28360232
Bioinformatics. 2009 Dec 15;25(24):3207-12
pubmed: 19808877
BMC Genomics. 2013 Aug 07;14:536
pubmed: 23919664
Bioinformatics. 2020 Jul 1;36(Suppl_1):i75-i83
pubmed: 32657355
PLoS One. 2011 Jan 31;6(1):e16685
pubmed: 21304912
Bioinformatics. 2021 May 1;37(4):456-463
pubmed: 32915952
Nature. 2020 Sep;585(7823):79-84
pubmed: 32663838
Nucleic Acids Res. 2012 Sep;40(16):e127
pubmed: 22584625
Nat Methods. 2019 Jan;16(1):88-94
pubmed: 30559433
BMC Bioinformatics. 2018 Feb 19;19(Suppl 1):45
pubmed: 29504909
Nat Biotechnol. 2022 Jul;40(7):1075-1081
pubmed: 35228706
Genome Res. 2017 May;27(5):849-864
pubmed: 28396521
Nat Biotechnol. 2020 Sep;38(9):1044-1053
pubmed: 32686750
PLoS Genet. 2019 Jul 26;15(7):e1008302
pubmed: 31348818
Am J Hum Genet. 2005 Jul;77(1):78-88
pubmed: 15918152
Bioinformatics. 2020 Jul 1;36(Suppl_1):i111-i118
pubmed: 32657365
Bioinformatics. 2017 Aug 01;33(15):2281-2287
pubmed: 28379292
Nat Commun. 2017 Jan 24;8:14061
pubmed: 28117401
Nat Methods. 2021 Feb;18(2):170-175
pubmed: 33526886
Genome Res. 2008 Nov;18(11):1851-8
pubmed: 18714091
Genome Biol. 2020 Oct 16;21(1):265
pubmed: 33066802
Nat Rev Genet. 2020 Mar;21(3):171-189
pubmed: 31729472
BMC Bioinformatics. 2012 Sep 19;13:238
pubmed: 22988817
Nat Commun. 2019 Apr 16;10(1):1784
pubmed: 30992455
Nat Commun. 2016 Apr 15;7:11307
pubmed: 27079541
Am J Hum Genet. 2003 Sep;73(3):591-600
pubmed: 12916016
Science. 2010 Oct 29;330(6004):641-6
pubmed: 21030649
Nucleic Acids Res. 2020 Nov 4;48(19):e114
pubmed: 33035301
J Comput Biol. 2018 Jul;25(7):766-779
pubmed: 29708767
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278