Flexible and efficient handling of nanopore sequencing signal data with slow5tools

Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow...
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Gespeichert in:

Autor*in:	Samarakoon, Hiruna [verfasserIn] Ferguson, James M. Jenner, Sasha P. Amos, Timothy G. Parameswaran, Sri Gamaarachchi, Hasindu Deveson, Ira W.

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	Nanopore sequencing Nanopore signal data SLOW5 Toolkit

Anmerkung:	© The Author(s) 2023

Übergeordnetes Werk:	Enthalten in: Genome biology - London : BioMed Central, 2000, 24(2023), 1 vom: 06. Apr.
Übergeordnetes Werk:	volume:24 ; year:2023 ; number:1 ; day:06 ; month:04

Links:	Volltext

DOI / URN:	10.1186/s13059-023-02910-3

Katalog-ID:	SPR049971972

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allfields	10.1186/s13059-023-02910-3 doi (DE-627)SPR049971972 (SPR)s13059-023-02910-3-e DE-627 ger DE-627 rakwb eng Samarakoon, Hiruna verfasserin aut Flexible and efficient handling of nanopore sequencing signal data with slow5tools 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance. Nanopore sequencing (dpeaa)DE-He213 Nanopore signal data (dpeaa)DE-He213 SLOW5 (dpeaa)DE-He213 Toolkit (dpeaa)DE-He213 Ferguson, James M. aut Jenner, Sasha P. aut Amos, Timothy G. aut Parameswaran, Sri aut Gamaarachchi, Hasindu aut Deveson, Ira W. (orcid)0000-0003-3861-0472 aut Enthalten in Genome biology London : BioMed Central, 2000 24(2023), 1 vom: 06. Apr. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:24 year:2023 number:1 day:06 month:04 https://dx.doi.org/10.1186/s13059-023-02910-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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_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_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 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 24 2023 1 06 04
spelling	10.1186/s13059-023-02910-3 doi (DE-627)SPR049971972 (SPR)s13059-023-02910-3-e DE-627 ger DE-627 rakwb eng Samarakoon, Hiruna verfasserin aut Flexible and efficient handling of nanopore sequencing signal data with slow5tools 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance. Nanopore sequencing (dpeaa)DE-He213 Nanopore signal data (dpeaa)DE-He213 SLOW5 (dpeaa)DE-He213 Toolkit (dpeaa)DE-He213 Ferguson, James M. aut Jenner, Sasha P. aut Amos, Timothy G. aut Parameswaran, Sri aut Gamaarachchi, Hasindu aut Deveson, Ira W. (orcid)0000-0003-3861-0472 aut Enthalten in Genome biology London : BioMed Central, 2000 24(2023), 1 vom: 06. Apr. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:24 year:2023 number:1 day:06 month:04 https://dx.doi.org/10.1186/s13059-023-02910-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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_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_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 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 24 2023 1 06 04
allfields_unstemmed	10.1186/s13059-023-02910-3 doi (DE-627)SPR049971972 (SPR)s13059-023-02910-3-e DE-627 ger DE-627 rakwb eng Samarakoon, Hiruna verfasserin aut Flexible and efficient handling of nanopore sequencing signal data with slow5tools 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance. Nanopore sequencing (dpeaa)DE-He213 Nanopore signal data (dpeaa)DE-He213 SLOW5 (dpeaa)DE-He213 Toolkit (dpeaa)DE-He213 Ferguson, James M. aut Jenner, Sasha P. aut Amos, Timothy G. aut Parameswaran, Sri aut Gamaarachchi, Hasindu aut Deveson, Ira W. (orcid)0000-0003-3861-0472 aut Enthalten in Genome biology London : BioMed Central, 2000 24(2023), 1 vom: 06. Apr. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:24 year:2023 number:1 day:06 month:04 https://dx.doi.org/10.1186/s13059-023-02910-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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_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_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 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 24 2023 1 06 04
allfieldsGer	10.1186/s13059-023-02910-3 doi (DE-627)SPR049971972 (SPR)s13059-023-02910-3-e DE-627 ger DE-627 rakwb eng Samarakoon, Hiruna verfasserin aut Flexible and efficient handling of nanopore sequencing signal data with slow5tools 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance. Nanopore sequencing (dpeaa)DE-He213 Nanopore signal data (dpeaa)DE-He213 SLOW5 (dpeaa)DE-He213 Toolkit (dpeaa)DE-He213 Ferguson, James M. aut Jenner, Sasha P. aut Amos, Timothy G. aut Parameswaran, Sri aut Gamaarachchi, Hasindu aut Deveson, Ira W. (orcid)0000-0003-3861-0472 aut Enthalten in Genome biology London : BioMed Central, 2000 24(2023), 1 vom: 06. Apr. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:24 year:2023 number:1 day:06 month:04 https://dx.doi.org/10.1186/s13059-023-02910-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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_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_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 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 24 2023 1 06 04
allfieldsSound	10.1186/s13059-023-02910-3 doi (DE-627)SPR049971972 (SPR)s13059-023-02910-3-e DE-627 ger DE-627 rakwb eng Samarakoon, Hiruna verfasserin aut Flexible and efficient handling of nanopore sequencing signal data with slow5tools 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance. Nanopore sequencing (dpeaa)DE-He213 Nanopore signal data (dpeaa)DE-He213 SLOW5 (dpeaa)DE-He213 Toolkit (dpeaa)DE-He213 Ferguson, James M. aut Jenner, Sasha P. aut Amos, Timothy G. aut Parameswaran, Sri aut Gamaarachchi, Hasindu aut Deveson, Ira W. (orcid)0000-0003-3861-0472 aut Enthalten in Genome biology London : BioMed Central, 2000 24(2023), 1 vom: 06. Apr. (DE-627)326173617 (DE-600)2040529-7 1474-760X nnns volume:24 year:2023 number:1 day:06 month:04 https://dx.doi.org/10.1186/s13059-023-02910-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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_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_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 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 24 2023 1 06 04
language	English
source	Enthalten in Genome biology 24(2023), 1 vom: 06. Apr. volume:24 year:2023 number:1 day:06 month:04
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author	Samarakoon, Hiruna
spellingShingle	Samarakoon, Hiruna misc Nanopore sequencing misc Nanopore signal data misc SLOW5 misc Toolkit Flexible and efficient handling of nanopore sequencing signal data with slow5tools
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topic_title	Flexible and efficient handling of nanopore sequencing signal data with slow5tools Nanopore sequencing (dpeaa)DE-He213 Nanopore signal data (dpeaa)DE-He213 SLOW5 (dpeaa)DE-He213 Toolkit (dpeaa)DE-He213
topic	misc Nanopore sequencing misc Nanopore signal data misc SLOW5 misc Toolkit
topic_unstemmed	misc Nanopore sequencing misc Nanopore signal data misc SLOW5 misc Toolkit
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title	Flexible and efficient handling of nanopore sequencing signal data with slow5tools
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title_full	Flexible and efficient handling of nanopore sequencing signal data with slow5tools
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author_browse	Samarakoon, Hiruna Ferguson, James M. Jenner, Sasha P. Amos, Timothy G. Parameswaran, Sri Gamaarachchi, Hasindu Deveson, Ira W.
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title_sort	flexible and efficient handling of nanopore sequencing signal data with slow5tools
title_auth	Flexible and efficient handling of nanopore sequencing signal data with slow5tools
abstract	Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance. © The Author(s) 2023
abstractGer	Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance. © The Author(s) 2023
abstract_unstemmed	Abstract Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance. © The Author(s) 2023
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title_short	Flexible and efficient handling of nanopore sequencing signal data with slow5tools
url	https://dx.doi.org/10.1186/s13059-023-02910-3
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author2	Ferguson, James M. Jenner, Sasha P. Amos, Timothy G. Parameswaran, Sri Gamaarachchi, Hasindu Deveson, Ira W.
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up_date	2024-07-04T02:58:32.222Z
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Flexible and efficient handling of nanopore sequencing signal data with slow5tools

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Zugang & Verfügbarkeit

Vorhandene Bände

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