The Experts below are selected from a list of 22995 Experts worldwide ranked by ideXlab platform
James K Bonfield - One of the best experts on this subject based on the ideXlab platform.
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twelve years of SAMtools and bcftools
GigaScience, 2021Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M Keane, Shane Mccarthy, Robert L DaviesAbstract:BACKGROUND SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. CONCLUSION Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.
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Twelve years of SAMtools and BCFtools.
GigaScience, 2021Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Andrew Whitwham, Martin O Pollard, Thomas Keane, Shane A Mccarthy, Robert M DaviesAbstract:SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org. © The Author(s) 2021. Published by Oxford University Press GigaScience.
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HTSlib: C library for reading/writing high-throughput sequencing data.
GigaScience, 2021Co-Authors: James K Bonfield, Petr Danecek, John Marshall, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M DaviesAbstract: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. 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. 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 >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. © The Author(s) 2021. Published by Oxford University Press GigaScience.
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twelve years of SAMtools and bcftools
arXiv: Genomics, 2020Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M Keane, Shane Mccarthy, Robert L DaviesAbstract:Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed over a million times via Bioconda. The source code and documentation are available from this http URL
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HTSlib - C library for reading/writing high-throughput sequencing data
2020Co-Authors: James K Bonfield, Petr Danecek, Valeriu Ohan, Andrew Whitwham, Thomas M Keane, John F. Marshall, Robert L DaviesAbstract:Abstract Background 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. Findings 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. Conclusion Since the original SAMtools release, performance has been considerably improved, with a BAM read-write loop running 4.9 times faster and BAM to SAM conversion at 12.8 times faster (both using 16 threads, compared to SAMtools 0.1.19). Widespread adoption has seen HTSlib downloaded over a 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.
Petr Danecek - One of the best experts on this subject based on the ideXlab platform.
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Twelve years of SAMtools and BCFtools.
GigaScience, 2021Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Andrew Whitwham, Martin O Pollard, Thomas Keane, Shane A Mccarthy, Robert M DaviesAbstract:SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org. © The Author(s) 2021. Published by Oxford University Press GigaScience.
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twelve years of SAMtools and bcftools
GigaScience, 2021Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M Keane, Shane Mccarthy, Robert L DaviesAbstract:BACKGROUND SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. CONCLUSION Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.
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HTSlib: C library for reading/writing high-throughput sequencing data.
GigaScience, 2021Co-Authors: James K Bonfield, Petr Danecek, John Marshall, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M DaviesAbstract: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. 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. 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 >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. © The Author(s) 2021. Published by Oxford University Press GigaScience.
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twelve years of SAMtools and bcftools
arXiv: Genomics, 2020Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M Keane, Shane Mccarthy, Robert L DaviesAbstract:Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed over a million times via Bioconda. The source code and documentation are available from this http URL
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HTSlib - C library for reading/writing high-throughput sequencing data
2020Co-Authors: James K Bonfield, Petr Danecek, Valeriu Ohan, Andrew Whitwham, Thomas M Keane, John F. Marshall, Robert L DaviesAbstract:Abstract Background 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. Findings 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. Conclusion Since the original SAMtools release, performance has been considerably improved, with a BAM read-write loop running 4.9 times faster and BAM to SAM conversion at 12.8 times faster (both using 16 threads, compared to SAMtools 0.1.19). Widespread adoption has seen HTSlib downloaded over a 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.
Robert M Davies - One of the best experts on this subject based on the ideXlab platform.
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Twelve years of SAMtools and BCFtools.
GigaScience, 2021Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Andrew Whitwham, Martin O Pollard, Thomas Keane, Shane A Mccarthy, Robert M DaviesAbstract:SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org. © The Author(s) 2021. Published by Oxford University Press GigaScience.
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HTSlib: C library for reading/writing high-throughput sequencing data.
GigaScience, 2021Co-Authors: James K Bonfield, Petr Danecek, John Marshall, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M DaviesAbstract: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. 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. 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 >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. © The Author(s) 2021. Published by Oxford University Press GigaScience.
Valeriu Ohan - One of the best experts on this subject based on the ideXlab platform.
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Twelve years of SAMtools and BCFtools.
GigaScience, 2021Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Andrew Whitwham, Martin O Pollard, Thomas Keane, Shane A Mccarthy, Robert M DaviesAbstract:SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org. © The Author(s) 2021. Published by Oxford University Press GigaScience.
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twelve years of SAMtools and bcftools
GigaScience, 2021Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M Keane, Shane Mccarthy, Robert L DaviesAbstract:BACKGROUND SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. CONCLUSION Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.
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HTSlib: C library for reading/writing high-throughput sequencing data.
GigaScience, 2021Co-Authors: James K Bonfield, Petr Danecek, John Marshall, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M DaviesAbstract: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. 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. 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 >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. © The Author(s) 2021. Published by Oxford University Press GigaScience.
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twelve years of SAMtools and bcftools
arXiv: Genomics, 2020Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M Keane, Shane Mccarthy, Robert L DaviesAbstract:Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed over a million times via Bioconda. The source code and documentation are available from this http URL
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HTSlib - C library for reading/writing high-throughput sequencing data
2020Co-Authors: James K Bonfield, Petr Danecek, Valeriu Ohan, Andrew Whitwham, Thomas M Keane, John F. Marshall, Robert L DaviesAbstract:Abstract Background 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. Findings 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. Conclusion Since the original SAMtools release, performance has been considerably improved, with a BAM read-write loop running 4.9 times faster and BAM to SAM conversion at 12.8 times faster (both using 16 threads, compared to SAMtools 0.1.19). Widespread adoption has seen HTSlib downloaded over a 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.
Andrew Whitwham - One of the best experts on this subject based on the ideXlab platform.
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Twelve years of SAMtools and BCFtools.
GigaScience, 2021Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Andrew Whitwham, Martin O Pollard, Thomas Keane, Shane A Mccarthy, Robert M DaviesAbstract:SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org. © The Author(s) 2021. Published by Oxford University Press GigaScience.
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twelve years of SAMtools and bcftools
GigaScience, 2021Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M Keane, Shane Mccarthy, Robert L DaviesAbstract:BACKGROUND SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. CONCLUSION Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.
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HTSlib: C library for reading/writing high-throughput sequencing data.
GigaScience, 2021Co-Authors: James K Bonfield, Petr Danecek, John Marshall, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M DaviesAbstract: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. 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. 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 >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. © The Author(s) 2021. Published by Oxford University Press GigaScience.
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twelve years of SAMtools and bcftools
arXiv: Genomics, 2020Co-Authors: Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin Pollard, Andrew Whitwham, Thomas M Keane, Shane Mccarthy, Robert L DaviesAbstract:Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed over a million times via Bioconda. The source code and documentation are available from this http URL
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HTSlib - C library for reading/writing high-throughput sequencing data
2020Co-Authors: James K Bonfield, Petr Danecek, Valeriu Ohan, Andrew Whitwham, Thomas M Keane, John F. Marshall, Robert L DaviesAbstract:Abstract Background 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. Findings 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. Conclusion Since the original SAMtools release, performance has been considerably improved, with a BAM read-write loop running 4.9 times faster and BAM to SAM conversion at 12.8 times faster (both using 16 threads, compared to SAMtools 0.1.19). Widespread adoption has seen HTSlib downloaded over a 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.
