AluMine: alignment-free method for the discovery of polymorphic Alu element insertions

Abstract Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Re...
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Autor*in:	Tarmo Puurand [verfasserIn] Viktoria Kukuškina [verfasserIn] Fanny-Dhelia Pajuste [verfasserIn] Maido Remm [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	Alu repeat element Mobile element insertions Alignment-free sequence analysis

Übergeordnetes Werk:	In: Mobile DNA - BMC, 2010, 10(2019), 1, Seite 13
Übergeordnetes Werk:	volume:10 ; year:2019 ; number:1 ; pages:13

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s13100-019-0174-3

Katalog-ID:	DOAJ001295322

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520			\|a Abstract Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours.
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allfields	10.1186/s13100-019-0174-3 doi (DE-627)DOAJ001295322 (DE-599)DOAJ39233ce8461147e697151abc2ba7650f DE-627 ger DE-627 rakwb eng QH426-470 Tarmo Puurand verfasserin aut AluMine: alignment-free method for the discovery of polymorphic Alu element insertions 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours. Alu repeat element Mobile element insertions Alignment-free sequence analysis Genetics Viktoria Kukuškina verfasserin aut Fanny-Dhelia Pajuste verfasserin aut Maido Remm verfasserin aut In Mobile DNA BMC, 2010 10(2019), 1, Seite 13 (DE-627)617812632 (DE-600)2536054-1 17598753 nnns volume:10 year:2019 number:1 pages:13 https://doi.org/10.1186/s13100-019-0174-3 kostenfrei https://doaj.org/article/39233ce8461147e697151abc2ba7650f kostenfrei http://link.springer.com/article/10.1186/s13100-019-0174-3 kostenfrei https://doaj.org/toc/1759-8753 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2019 1 13
spelling	10.1186/s13100-019-0174-3 doi (DE-627)DOAJ001295322 (DE-599)DOAJ39233ce8461147e697151abc2ba7650f DE-627 ger DE-627 rakwb eng QH426-470 Tarmo Puurand verfasserin aut AluMine: alignment-free method for the discovery of polymorphic Alu element insertions 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours. Alu repeat element Mobile element insertions Alignment-free sequence analysis Genetics Viktoria Kukuškina verfasserin aut Fanny-Dhelia Pajuste verfasserin aut Maido Remm verfasserin aut In Mobile DNA BMC, 2010 10(2019), 1, Seite 13 (DE-627)617812632 (DE-600)2536054-1 17598753 nnns volume:10 year:2019 number:1 pages:13 https://doi.org/10.1186/s13100-019-0174-3 kostenfrei https://doaj.org/article/39233ce8461147e697151abc2ba7650f kostenfrei http://link.springer.com/article/10.1186/s13100-019-0174-3 kostenfrei https://doaj.org/toc/1759-8753 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2019 1 13
allfields_unstemmed	10.1186/s13100-019-0174-3 doi (DE-627)DOAJ001295322 (DE-599)DOAJ39233ce8461147e697151abc2ba7650f DE-627 ger DE-627 rakwb eng QH426-470 Tarmo Puurand verfasserin aut AluMine: alignment-free method for the discovery of polymorphic Alu element insertions 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours. Alu repeat element Mobile element insertions Alignment-free sequence analysis Genetics Viktoria Kukuškina verfasserin aut Fanny-Dhelia Pajuste verfasserin aut Maido Remm verfasserin aut In Mobile DNA BMC, 2010 10(2019), 1, Seite 13 (DE-627)617812632 (DE-600)2536054-1 17598753 nnns volume:10 year:2019 number:1 pages:13 https://doi.org/10.1186/s13100-019-0174-3 kostenfrei https://doaj.org/article/39233ce8461147e697151abc2ba7650f kostenfrei http://link.springer.com/article/10.1186/s13100-019-0174-3 kostenfrei https://doaj.org/toc/1759-8753 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2019 1 13
allfieldsGer	10.1186/s13100-019-0174-3 doi (DE-627)DOAJ001295322 (DE-599)DOAJ39233ce8461147e697151abc2ba7650f DE-627 ger DE-627 rakwb eng QH426-470 Tarmo Puurand verfasserin aut AluMine: alignment-free method for the discovery of polymorphic Alu element insertions 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours. Alu repeat element Mobile element insertions Alignment-free sequence analysis Genetics Viktoria Kukuškina verfasserin aut Fanny-Dhelia Pajuste verfasserin aut Maido Remm verfasserin aut In Mobile DNA BMC, 2010 10(2019), 1, Seite 13 (DE-627)617812632 (DE-600)2536054-1 17598753 nnns volume:10 year:2019 number:1 pages:13 https://doi.org/10.1186/s13100-019-0174-3 kostenfrei https://doaj.org/article/39233ce8461147e697151abc2ba7650f kostenfrei http://link.springer.com/article/10.1186/s13100-019-0174-3 kostenfrei https://doaj.org/toc/1759-8753 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2019 1 13
allfieldsSound	10.1186/s13100-019-0174-3 doi (DE-627)DOAJ001295322 (DE-599)DOAJ39233ce8461147e697151abc2ba7650f DE-627 ger DE-627 rakwb eng QH426-470 Tarmo Puurand verfasserin aut AluMine: alignment-free method for the discovery of polymorphic Alu element insertions 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours. Alu repeat element Mobile element insertions Alignment-free sequence analysis Genetics Viktoria Kukuškina verfasserin aut Fanny-Dhelia Pajuste verfasserin aut Maido Remm verfasserin aut In Mobile DNA BMC, 2010 10(2019), 1, Seite 13 (DE-627)617812632 (DE-600)2536054-1 17598753 nnns volume:10 year:2019 number:1 pages:13 https://doi.org/10.1186/s13100-019-0174-3 kostenfrei https://doaj.org/article/39233ce8461147e697151abc2ba7650f kostenfrei http://link.springer.com/article/10.1186/s13100-019-0174-3 kostenfrei https://doaj.org/toc/1759-8753 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2019 1 13
language	English
source	In Mobile DNA 10(2019), 1, Seite 13 volume:10 year:2019 number:1 pages:13
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institution	findex.gbv.de
topic_facet	Alu repeat element Mobile element insertions Alignment-free sequence analysis Genetics
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authorswithroles_txt_mv	Tarmo Puurand @@aut@@ Viktoria Kukuškina @@aut@@ Fanny-Dhelia Pajuste @@aut@@ Maido Remm @@aut@@
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These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. 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callnumber-first	Q - Science
author	Tarmo Puurand
spellingShingle	Tarmo Puurand misc QH426-470 misc Alu repeat element misc Mobile element insertions misc Alignment-free sequence analysis misc Genetics AluMine: alignment-free method for the discovery of polymorphic Alu element insertions
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topic_title	QH426-470 AluMine: alignment-free method for the discovery of polymorphic Alu element insertions Alu repeat element Mobile element insertions Alignment-free sequence analysis
topic	misc QH426-470 misc Alu repeat element misc Mobile element insertions misc Alignment-free sequence analysis misc Genetics
topic_unstemmed	misc QH426-470 misc Alu repeat element misc Mobile element insertions misc Alignment-free sequence analysis misc Genetics
topic_browse	misc QH426-470 misc Alu repeat element misc Mobile element insertions misc Alignment-free sequence analysis misc Genetics
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title	AluMine: alignment-free method for the discovery of polymorphic Alu element insertions
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title_full	AluMine: alignment-free method for the discovery of polymorphic Alu element insertions
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author_browse	Tarmo Puurand Viktoria Kukuškina Fanny-Dhelia Pajuste Maido Remm
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title_sort	alumine: alignment-free method for the discovery of polymorphic alu element insertions
callnumber	QH426-470
title_auth	AluMine: alignment-free method for the discovery of polymorphic Alu element insertions
abstract	Abstract Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours.
abstractGer	Abstract Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours.
abstract_unstemmed	Abstract Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours.
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title_short	AluMine: alignment-free method for the discovery of polymorphic Alu element insertions
url	https://doi.org/10.1186/s13100-019-0174-3 https://doaj.org/article/39233ce8461147e697151abc2ba7650f http://link.springer.com/article/10.1186/s13100-019-0174-3 https://doaj.org/toc/1759-8753
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author2	Viktoria Kukuškina Fanny-Dhelia Pajuste Maido Remm
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up_date	2024-07-03T19:34:52.172Z
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AluMine: alignment-free method for the discovery of polymorphic Alu element insertions

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