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HTSlib: C library for reading/writing high-throughput sequencing data

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Zeitschriftentitel: GigaScience
Personen und Körperschaften: Bonfield, James K, Marshall, John, Danecek, Petr, Li, Heng, Ohan, Valeriu, Whitwham, Andrew, Keane, Thomas, Davies, Robert M
In: GigaScience, 10, 2021, 2
Format: E-Article
Sprache: Englisch
veröffentlicht:
Oxford University Press (OUP)
Schlagwörter:
Computer Science Applications
Health Informatics
author_facet Bonfield, James K
Marshall, John
Danecek, Petr
Li, Heng
Ohan, Valeriu
Whitwham, Andrew
Keane, Thomas
Davies, Robert M
Bonfield, James K
Marshall, John
Danecek, Petr
Li, Heng
Ohan, Valeriu
Whitwham, Andrew
Keane, Thomas
Davies, Robert M
author Bonfield, James K
Marshall, John
Danecek, Petr
Li, Heng
Ohan, Valeriu
Whitwham, Andrew
Keane, Thomas
Davies, Robert M
spellingShingle Bonfield, James K
Marshall, John
Danecek, Petr
Li, Heng
Ohan, Valeriu
Whitwham, Andrew
Keane, Thomas
Davies, Robert M
GigaScience
HTSlib: C library for reading/writing high-throughput sequencing data
Computer Science Applications
Health Informatics
author_sort bonfield, james k
spelling Bonfield, James K Marshall, John Danecek, Petr Li, Heng Ohan, Valeriu Whitwham, Andrew Keane, Thomas Davies, Robert M 2047-217X Oxford University Press (OUP) Computer Science Applications Health Informatics http://dx.doi.org/10.1093/gigascience/giab007 <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.</jats:p> </jats:sec> <jats:sec> <jats:title>Findings</jats:title> <jats:p>We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusion</jats:title> <jats:p>Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded &amp;gt;1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.</jats:p> </jats:sec> HTSlib: C library for reading/writing high-throughput sequencing data GigaScience
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title HTSlib: C library for reading/writing high-throughput sequencing data
title_unstemmed HTSlib: C library for reading/writing high-throughput sequencing data
title_full HTSlib: C library for reading/writing high-throughput sequencing data
title_fullStr HTSlib: C library for reading/writing high-throughput sequencing data
title_full_unstemmed HTSlib: C library for reading/writing high-throughput sequencing data
title_short HTSlib: C library for reading/writing high-throughput sequencing data
title_sort htslib: c library for reading/writing high-throughput sequencing data
topic Computer Science Applications
Health Informatics
url http://dx.doi.org/10.1093/gigascience/giab007
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description <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.</jats:p> </jats:sec> <jats:sec> <jats:title>Findings</jats:title> <jats:p>We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusion</jats:title> <jats:p>Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded &amp;gt;1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.</jats:p> </jats:sec>
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author Bonfield, James K, Marshall, John, Danecek, Petr, Li, Heng, Ohan, Valeriu, Whitwham, Andrew, Keane, Thomas, Davies, Robert M
author_facet Bonfield, James K, Marshall, John, Danecek, Petr, Li, Heng, Ohan, Valeriu, Whitwham, Andrew, Keane, Thomas, Davies, Robert M, Bonfield, James K, Marshall, John, Danecek, Petr, Li, Heng, Ohan, Valeriu, Whitwham, Andrew, Keane, Thomas, Davies, Robert M
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description <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.</jats:p> </jats:sec> <jats:sec> <jats:title>Findings</jats:title> <jats:p>We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusion</jats:title> <jats:p>Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded &amp;gt;1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.</jats:p> </jats:sec>
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spelling Bonfield, James K Marshall, John Danecek, Petr Li, Heng Ohan, Valeriu Whitwham, Andrew Keane, Thomas Davies, Robert M 2047-217X Oxford University Press (OUP) Computer Science Applications Health Informatics http://dx.doi.org/10.1093/gigascience/giab007 <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.</jats:p> </jats:sec> <jats:sec> <jats:title>Findings</jats:title> <jats:p>We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusion</jats:title> <jats:p>Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded &amp;gt;1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.</jats:p> </jats:sec> HTSlib: C library for reading/writing high-throughput sequencing data GigaScience
spellingShingle Bonfield, James K, Marshall, John, Danecek, Petr, Li, Heng, Ohan, Valeriu, Whitwham, Andrew, Keane, Thomas, Davies, Robert M, GigaScience, HTSlib: C library for reading/writing high-throughput sequencing data, Computer Science Applications, Health Informatics
title HTSlib: C library for reading/writing high-throughput sequencing data
title_full HTSlib: C library for reading/writing high-throughput sequencing data
title_fullStr HTSlib: C library for reading/writing high-throughput sequencing data
title_full_unstemmed HTSlib: C library for reading/writing high-throughput sequencing data
title_short HTSlib: C library for reading/writing high-throughput sequencing data
title_sort htslib: c library for reading/writing high-throughput sequencing data
title_unstemmed HTSlib: C library for reading/writing high-throughput sequencing data
topic Computer Science Applications, Health Informatics
url http://dx.doi.org/10.1093/gigascience/giab007