STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data

Abstract Background Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches e...
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Autor*in:	Mattia Dalsass [verfasserIn] Margherita Bodini [verfasserIn] Christophe Lambert [verfasserIn] Marie-Cécile Mortier [verfasserIn] Marco Romanelli [verfasserIn] Duccio Medini [verfasserIn] Alessandro Muzzi [verfasserIn] Alessandro Brozzi [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2019

Schlagwörter:	Whole genome sequencing (WGS) Multi locus sequence type (MLST) Sequence type (ST) R package

Übergeordnetes Werk:	In: BMC Bioinformatics - BMC, 2003, 20(2019), S9, Seite 8
Übergeordnetes Werk:	volume:20 ; year:2019 ; number:S9 ; pages:8

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s12859-019-2887-1

Katalog-ID:	DOAJ039321053

Internformat


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520			\|a Abstract Background Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses.
650		4	\|a Whole genome sequencing (WGS)
650		4	\|a Multi locus sequence type (MLST)
650		4	\|a Sequence type (ST)
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653		0	\|a Computer applications to medicine. Medical informatics
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700	0		\|a Margherita Bodini \|e verfasserin \|4 aut
700	0		\|a Christophe Lambert \|e verfasserin \|4 aut
700	0		\|a Marie-Cécile Mortier \|e verfasserin \|4 aut
700	0		\|a Marco Romanelli \|e verfasserin \|4 aut
700	0		\|a Duccio Medini \|e verfasserin \|4 aut
700	0		\|a Alessandro Muzzi \|e verfasserin \|4 aut
700	0		\|a Alessandro Brozzi \|e verfasserin \|4 aut
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912			\|a GBV_ILN_285
912			\|a GBV_ILN_293
912			\|a GBV_ILN_370
912			\|a GBV_ILN_602
912			\|a GBV_ILN_702
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912			\|a GBV_ILN_4325
912			\|a GBV_ILN_4326
912			\|a GBV_ILN_4335
912			\|a GBV_ILN_4338
912			\|a GBV_ILN_4367
912			\|a GBV_ILN_4700
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allfields	10.1186/s12859-019-2887-1 doi (DE-627)DOAJ039321053 (DE-599)DOAJ3d5a5ad0ad2d49f484d568fdb9e4fb52 DE-627 ger DE-627 rakwb eng R858-859.7 QH301-705.5 Mattia Dalsass verfasserin aut STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses. Whole genome sequencing (WGS) Multi locus sequence type (MLST) Sequence type (ST) R package Computer applications to medicine. Medical informatics Biology (General) Margherita Bodini verfasserin aut Christophe Lambert verfasserin aut Marie-Cécile Mortier verfasserin aut Marco Romanelli verfasserin aut Duccio Medini verfasserin aut Alessandro Muzzi verfasserin aut Alessandro Brozzi verfasserin aut In BMC Bioinformatics BMC, 2003 20(2019), S9, Seite 8 (DE-627)326644814 (DE-600)2041484-5 14712105 nnns volume:20 year:2019 number:S9 pages:8 https://doi.org/10.1186/s12859-019-2887-1 kostenfrei https://doaj.org/article/3d5a5ad0ad2d49f484d568fdb9e4fb52 kostenfrei http://link.springer.com/article/10.1186/s12859-019-2887-1 kostenfrei https://doaj.org/toc/1471-2105 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_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 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_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 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_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 S9 8
spelling	10.1186/s12859-019-2887-1 doi (DE-627)DOAJ039321053 (DE-599)DOAJ3d5a5ad0ad2d49f484d568fdb9e4fb52 DE-627 ger DE-627 rakwb eng R858-859.7 QH301-705.5 Mattia Dalsass verfasserin aut STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses. Whole genome sequencing (WGS) Multi locus sequence type (MLST) Sequence type (ST) R package Computer applications to medicine. Medical informatics Biology (General) Margherita Bodini verfasserin aut Christophe Lambert verfasserin aut Marie-Cécile Mortier verfasserin aut Marco Romanelli verfasserin aut Duccio Medini verfasserin aut Alessandro Muzzi verfasserin aut Alessandro Brozzi verfasserin aut In BMC Bioinformatics BMC, 2003 20(2019), S9, Seite 8 (DE-627)326644814 (DE-600)2041484-5 14712105 nnns volume:20 year:2019 number:S9 pages:8 https://doi.org/10.1186/s12859-019-2887-1 kostenfrei https://doaj.org/article/3d5a5ad0ad2d49f484d568fdb9e4fb52 kostenfrei http://link.springer.com/article/10.1186/s12859-019-2887-1 kostenfrei https://doaj.org/toc/1471-2105 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_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 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_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 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_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 S9 8
allfields_unstemmed	10.1186/s12859-019-2887-1 doi (DE-627)DOAJ039321053 (DE-599)DOAJ3d5a5ad0ad2d49f484d568fdb9e4fb52 DE-627 ger DE-627 rakwb eng R858-859.7 QH301-705.5 Mattia Dalsass verfasserin aut STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses. Whole genome sequencing (WGS) Multi locus sequence type (MLST) Sequence type (ST) R package Computer applications to medicine. Medical informatics Biology (General) Margherita Bodini verfasserin aut Christophe Lambert verfasserin aut Marie-Cécile Mortier verfasserin aut Marco Romanelli verfasserin aut Duccio Medini verfasserin aut Alessandro Muzzi verfasserin aut Alessandro Brozzi verfasserin aut In BMC Bioinformatics BMC, 2003 20(2019), S9, Seite 8 (DE-627)326644814 (DE-600)2041484-5 14712105 nnns volume:20 year:2019 number:S9 pages:8 https://doi.org/10.1186/s12859-019-2887-1 kostenfrei https://doaj.org/article/3d5a5ad0ad2d49f484d568fdb9e4fb52 kostenfrei http://link.springer.com/article/10.1186/s12859-019-2887-1 kostenfrei https://doaj.org/toc/1471-2105 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_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 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_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 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_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 S9 8
allfieldsGer	10.1186/s12859-019-2887-1 doi (DE-627)DOAJ039321053 (DE-599)DOAJ3d5a5ad0ad2d49f484d568fdb9e4fb52 DE-627 ger DE-627 rakwb eng R858-859.7 QH301-705.5 Mattia Dalsass verfasserin aut STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses. Whole genome sequencing (WGS) Multi locus sequence type (MLST) Sequence type (ST) R package Computer applications to medicine. Medical informatics Biology (General) Margherita Bodini verfasserin aut Christophe Lambert verfasserin aut Marie-Cécile Mortier verfasserin aut Marco Romanelli verfasserin aut Duccio Medini verfasserin aut Alessandro Muzzi verfasserin aut Alessandro Brozzi verfasserin aut In BMC Bioinformatics BMC, 2003 20(2019), S9, Seite 8 (DE-627)326644814 (DE-600)2041484-5 14712105 nnns volume:20 year:2019 number:S9 pages:8 https://doi.org/10.1186/s12859-019-2887-1 kostenfrei https://doaj.org/article/3d5a5ad0ad2d49f484d568fdb9e4fb52 kostenfrei http://link.springer.com/article/10.1186/s12859-019-2887-1 kostenfrei https://doaj.org/toc/1471-2105 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_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 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_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 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_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 S9 8
allfieldsSound	10.1186/s12859-019-2887-1 doi (DE-627)DOAJ039321053 (DE-599)DOAJ3d5a5ad0ad2d49f484d568fdb9e4fb52 DE-627 ger DE-627 rakwb eng R858-859.7 QH301-705.5 Mattia Dalsass verfasserin aut STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses. Whole genome sequencing (WGS) Multi locus sequence type (MLST) Sequence type (ST) R package Computer applications to medicine. Medical informatics Biology (General) Margherita Bodini verfasserin aut Christophe Lambert verfasserin aut Marie-Cécile Mortier verfasserin aut Marco Romanelli verfasserin aut Duccio Medini verfasserin aut Alessandro Muzzi verfasserin aut Alessandro Brozzi verfasserin aut In BMC Bioinformatics BMC, 2003 20(2019), S9, Seite 8 (DE-627)326644814 (DE-600)2041484-5 14712105 nnns volume:20 year:2019 number:S9 pages:8 https://doi.org/10.1186/s12859-019-2887-1 kostenfrei https://doaj.org/article/3d5a5ad0ad2d49f484d568fdb9e4fb52 kostenfrei http://link.springer.com/article/10.1186/s12859-019-2887-1 kostenfrei https://doaj.org/toc/1471-2105 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_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 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_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 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_4326 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 20 2019 S9 8
language	English
source	In BMC Bioinformatics 20(2019), S9, Seite 8 volume:20 year:2019 number:S9 pages:8
sourceStr	In BMC Bioinformatics 20(2019), S9, Seite 8 volume:20 year:2019 number:S9 pages:8
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Whole genome sequencing (WGS) Multi locus sequence type (MLST) Sequence type (ST) R package Computer applications to medicine. Medical informatics Biology (General)
isfreeaccess_bool	true
container_title	BMC Bioinformatics
authorswithroles_txt_mv	Mattia Dalsass @@aut@@ Margherita Bodini @@aut@@ Christophe Lambert @@aut@@ Marie-Cécile Mortier @@aut@@ Marco Romanelli @@aut@@ Duccio Medini @@aut@@ Alessandro Muzzi @@aut@@ Alessandro Brozzi @@aut@@
publishDateDaySort_date	2019-01-01T00:00:00Z
hierarchy_top_id	326644814
id	DOAJ039321053
language_de	englisch
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When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. 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callnumber-first	R - Medicine
author	Mattia Dalsass
spellingShingle	Mattia Dalsass misc R858-859.7 misc QH301-705.5 misc Whole genome sequencing (WGS) misc Multi locus sequence type (MLST) misc Sequence type (ST) misc R package misc Computer applications to medicine. Medical informatics misc Biology (General) STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data
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topic_title	R858-859.7 QH301-705.5 STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data Whole genome sequencing (WGS) Multi locus sequence type (MLST) Sequence type (ST) R package
topic	misc R858-859.7 misc QH301-705.5 misc Whole genome sequencing (WGS) misc Multi locus sequence type (MLST) misc Sequence type (ST) misc R package misc Computer applications to medicine. Medical informatics misc Biology (General)
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title	STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data
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title_full	STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data
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author_browse	Mattia Dalsass Margherita Bodini Christophe Lambert Marie-Cécile Mortier Marco Romanelli Duccio Medini Alessandro Muzzi Alessandro Brozzi
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title_sort	strain: an r package for multi-locus sequence typing from whole genome sequencing data
callnumber	R858-859.7
title_auth	STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data
abstract	Abstract Background Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses.
abstractGer	Abstract Background Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses.
abstract_unstemmed	Abstract Background Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses.
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title_short	STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data
url	https://doi.org/10.1186/s12859-019-2887-1 https://doaj.org/article/3d5a5ad0ad2d49f484d568fdb9e4fb52 http://link.springer.com/article/10.1186/s12859-019-2887-1 https://doaj.org/toc/1471-2105
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When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. Results Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). Conclusions STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Whole genome sequencing (WGS)</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Multi locus sequence type (MLST)</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Sequence type (ST)</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">R package</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Computer applications to medicine. 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STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data

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