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George M. Garrity - One of the best experts on this subject based on the ideXlab platform.

  • Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)
    Standards in Genomic Sciences, 2016
    Co-Authors: Scott Federhen, Ramon Rosselló-móra, Hans-peter Klenk, Brian J. Tindall, Konstantinos T. Konstantinidis, William B. Whitman, Daniel R. Brown, David P. Labeda, David W. Ussery, George M. Garrity
    Abstract:

    Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes from type. A workshop was organized with broad representation from the bacterial taxonomic community to review the proposal, the GenBank Microbial Genomic Taxonomy Workshop, Bethesda MD, May 12–13, 2015.

  • meeting report GenBank microbial genomic taxonomy workshop 12 13 may 2015
    Standards in Genomic Sciences, 2016
    Co-Authors: Scott Federhen, Hans-peter Klenk, Brian J. Tindall, Konstantinos T. Konstantinidis, William B. Whitman, Daniel R. Brown, David P. Labeda, David W. Ussery, Ramon Rossellomora, George M. Garrity
    Abstract:

    Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes from type. A workshop was organized with broad representation from the bacterial taxonomic community to review the proposal, the GenBank Microbial Genomic Taxonomy Workshop, Bethesda MD, May 12–13, 2015.

Alexander L. Greninger - One of the best experts on this subject based on the ideXlab platform.

  • vapid a lightweight cross platform viral annotation pipeline and identification tool to facilitate virus genome submissions to ncbi GenBank
    BMC Bioinformatics, 2019
    Co-Authors: Ryan C. Shean, Negar Makhsous, Graham D. Stoddard, Michelle J. Lin, Alexander L. Greninger
    Abstract:

    Background With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available. GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.

  • VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank
    BMC, 2019
    Co-Authors: Ryan C. Shean, Negar Makhsous, Graham D. Stoddard, Michelle J. Lin, Alexander L. Greninger
    Abstract:

    Abstract Background With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available. GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions. Results We present Viral Annotation Pipeline and iDentification (VAPiD), a portable and lightweight command-line tool for annotation and GenBank deposition of viral genomes. VAPiD supports annotation of nearly all unsegmented viral genomes. The pipeline has been validated on human immunodeficiency virus, human parainfluenza virus 1–4, human metapneumovirus, human coronaviruses (229E/OC43/NL63/HKU1/SARS/MERS), human enteroviruses/rhinoviruses, measles virus, mumps virus, Hepatitis A-E Virus, Chikungunya virus, dengue virus, and West Nile virus, as well the human polyomaviruses BK/JC/MCV, human adenoviruses, and human papillomaviruses. The program can handle individual or batch submissions of different viruses to GenBank and correctly annotates multiple viruses, including those that contain ribosomal slippage or RNA editing without prior knowledge of the virus to be annotated. VAPiD is programmed in Python and is compatible with Windows, Linux, and Mac OS systems. Conclusions We have created a portable, lightweight, user-friendly, internet-enabled, open-source, command-line genome annotation and submission package to facilitate virus genome submissions to NCBI GenBank. Instructions for downloading and installing VAPiD can be found at https://github.com/rcs333/VAPiD

Scott Federhen - One of the best experts on this subject based on the ideXlab platform.

  • Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)
    Standards in Genomic Sciences, 2016
    Co-Authors: Scott Federhen, Ramon Rosselló-móra, Hans-peter Klenk, Brian J. Tindall, Konstantinos T. Konstantinidis, William B. Whitman, Daniel R. Brown, David P. Labeda, David W. Ussery, George M. Garrity
    Abstract:

    Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes from type. A workshop was organized with broad representation from the bacterial taxonomic community to review the proposal, the GenBank Microbial Genomic Taxonomy Workshop, Bethesda MD, May 12–13, 2015.

  • meeting report GenBank microbial genomic taxonomy workshop 12 13 may 2015
    Standards in Genomic Sciences, 2016
    Co-Authors: Scott Federhen, Hans-peter Klenk, Brian J. Tindall, Konstantinos T. Konstantinidis, William B. Whitman, Daniel R. Brown, David P. Labeda, David W. Ussery, Ramon Rossellomora, George M. Garrity
    Abstract:

    Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes from type. A workshop was organized with broad representation from the bacterial taxonomic community to review the proposal, the GenBank Microbial Genomic Taxonomy Workshop, Bethesda MD, May 12–13, 2015.

Ryan C. Shean - One of the best experts on this subject based on the ideXlab platform.

  • vapid a lightweight cross platform viral annotation pipeline and identification tool to facilitate virus genome submissions to ncbi GenBank
    BMC Bioinformatics, 2019
    Co-Authors: Ryan C. Shean, Negar Makhsous, Graham D. Stoddard, Michelle J. Lin, Alexander L. Greninger
    Abstract:

    Background With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available. GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.

  • VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank
    BMC, 2019
    Co-Authors: Ryan C. Shean, Negar Makhsous, Graham D. Stoddard, Michelle J. Lin, Alexander L. Greninger
    Abstract:

    Abstract Background With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available. GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions. Results We present Viral Annotation Pipeline and iDentification (VAPiD), a portable and lightweight command-line tool for annotation and GenBank deposition of viral genomes. VAPiD supports annotation of nearly all unsegmented viral genomes. The pipeline has been validated on human immunodeficiency virus, human parainfluenza virus 1–4, human metapneumovirus, human coronaviruses (229E/OC43/NL63/HKU1/SARS/MERS), human enteroviruses/rhinoviruses, measles virus, mumps virus, Hepatitis A-E Virus, Chikungunya virus, dengue virus, and West Nile virus, as well the human polyomaviruses BK/JC/MCV, human adenoviruses, and human papillomaviruses. The program can handle individual or batch submissions of different viruses to GenBank and correctly annotates multiple viruses, including those that contain ribosomal slippage or RNA editing without prior knowledge of the virus to be annotated. VAPiD is programmed in Python and is compatible with Windows, Linux, and Mac OS systems. Conclusions We have created a portable, lightweight, user-friendly, internet-enabled, open-source, command-line genome annotation and submission package to facilitate virus genome submissions to NCBI GenBank. Instructions for downloading and installing VAPiD can be found at https://github.com/rcs333/VAPiD

William B. Whitman - One of the best experts on this subject based on the ideXlab platform.

  • Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)
    Standards in Genomic Sciences, 2016
    Co-Authors: Scott Federhen, Ramon Rosselló-móra, Hans-peter Klenk, Brian J. Tindall, Konstantinos T. Konstantinidis, William B. Whitman, Daniel R. Brown, David P. Labeda, David W. Ussery, George M. Garrity
    Abstract:

    Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes from type. A workshop was organized with broad representation from the bacterial taxonomic community to review the proposal, the GenBank Microbial Genomic Taxonomy Workshop, Bethesda MD, May 12–13, 2015.

  • meeting report GenBank microbial genomic taxonomy workshop 12 13 may 2015
    Standards in Genomic Sciences, 2016
    Co-Authors: Scott Federhen, Hans-peter Klenk, Brian J. Tindall, Konstantinos T. Konstantinidis, William B. Whitman, Daniel R. Brown, David P. Labeda, David W. Ussery, Ramon Rossellomora, George M. Garrity
    Abstract:

    Many genomes are incorrectly identified at GenBank. We developed a plan to find and correct misidentified genomes using genomic comparison statistics together with a scaffold of reliably identified genomes from type. A workshop was organized with broad representation from the bacterial taxonomic community to review the proposal, the GenBank Microbial Genomic Taxonomy Workshop, Bethesda MD, May 12–13, 2015.