AlmostSignificant: simplifying quality control of high-throughput sequencing data

Joseph Ward; Christian Cole; Melanie Febrer; Geoffrey J. Barton

doi:10.1093/bioinformatics/btw559

AlmostSignificant: simplifying quality control of high-throughput sequencing data

Joseph Ward, Christian Cole (Lead / Corresponding author), Melanie Febrer, Geoffrey J. Barton (Lead / Corresponding author)

Computational Biology

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

88 Downloads (Pure)

Abstract

Motivation: The current generation of DNA sequencing technologies produce a large amount of data quickly. All of these data need to pass some form of quality control (QC) processing and checking before they can be used for any analysis. The large number of samples that are run through Illumina sequencing machines makes the process of QC an onerous and time-consuming task that requires multiple pieces of information from several sources.

Results: AlmostSignificant is an open-source platform for aggregating multiple sources of quality metrics as well as run and sample meta-data associated with DNA sequencing runs from Illumina sequencing machines. AlmostSignificant is a graphical platform to streamline the QC of DNA sequencing data, to store these data for future reference together with extra meta-data associated with the sequencing runs not typically retained. This simplifies the challenge of monitoring the volume of data produced by Illumina sequencers. AlmostSignificant has been used to track the quality of over 80 sequencing runs covering over 2500 samples produced over the last three years.

Availability: The code and documentation for AlmostSignificant is freely available at https://github.com/bartongroup/AlmostSignificant CONTACT: c.cole@dundee.ac.uk, g.j.barton@dundee.ac.uk.

Original language	English
Pages (from-to)	3850-3851
Number of pages	2
Journal	Bioinformatics
Volume	32
Issue number	24
Early online date	24 Aug 2016
DOIs	https://doi.org/10.1093/bioinformatics/btw559
Publication status	Published - 15 Dec 2016

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10.1093/bioinformatics/btw559Licence: CC BY

Final Published Version
© The Author(s) 2016. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 262 KBLicence: CC BY

3 Citations
1 Preprint

AlmostSignificant: Simplifying quality control of high-throughput sequencing data
Ward, J., Cole, C., Febrer, M. & Barton, G., 16 May 2016, Cold Spring Harbor Laboratory: BioRxiv, 2 p.
Research output: Working paper/Preprint › Preprint

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Cole, Christian
- Population Health and Genomics - Senior Lecturer (Teaching and Research)
Person: Academic

Cite this

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title = "AlmostSignificant: simplifying quality control of high-throughput sequencing data",

abstract = "Motivation: The current generation of DNA sequencing technologies produce a large amount of data quickly. All of these data need to pass some form of quality control (QC) processing and checking before they can be used for any analysis. The large number of samples that are run through Illumina sequencing machines makes the process of QC an onerous and time-consuming task that requires multiple pieces of information from several sources.Results: AlmostSignificant is an open-source platform for aggregating multiple sources of quality metrics as well as run and sample meta-data associated with DNA sequencing runs from Illumina sequencing machines. AlmostSignificant is a graphical platform to streamline the QC of DNA sequencing data, to store these data for future reference together with extra meta-data associated with the sequencing runs not typically retained. This simplifies the challenge of monitoring the volume of data produced by Illumina sequencers. AlmostSignificant has been used to track the quality of over 80 sequencing runs covering over 2500 samples produced over the last three years.Availability: The code and documentation for AlmostSignificant is freely available at https://github.com/bartongroup/AlmostSignificant CONTACT: c.cole@dundee.ac.uk, g.j.barton@dundee.ac.uk.",

author = "Joseph Ward and Christian Cole and Melanie Febrer and Barton, {Geoffrey J.}",

note = "This work was supported by the Wellcome Trust Strategic Award 098439/Z/12/Z",

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doi = "10.1093/bioinformatics/btw559",

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T2 - simplifying quality control of high-throughput sequencing data

AU - Ward, Joseph

AU - Cole, Christian

AU - Febrer, Melanie

AU - Barton, Geoffrey J.

N1 - This work was supported by the Wellcome Trust Strategic Award 098439/Z/12/Z

PY - 2016/12/15

Y1 - 2016/12/15

N2 - Motivation: The current generation of DNA sequencing technologies produce a large amount of data quickly. All of these data need to pass some form of quality control (QC) processing and checking before they can be used for any analysis. The large number of samples that are run through Illumina sequencing machines makes the process of QC an onerous and time-consuming task that requires multiple pieces of information from several sources.Results: AlmostSignificant is an open-source platform for aggregating multiple sources of quality metrics as well as run and sample meta-data associated with DNA sequencing runs from Illumina sequencing machines. AlmostSignificant is a graphical platform to streamline the QC of DNA sequencing data, to store these data for future reference together with extra meta-data associated with the sequencing runs not typically retained. This simplifies the challenge of monitoring the volume of data produced by Illumina sequencers. AlmostSignificant has been used to track the quality of over 80 sequencing runs covering over 2500 samples produced over the last three years.Availability: The code and documentation for AlmostSignificant is freely available at https://github.com/bartongroup/AlmostSignificant CONTACT: c.cole@dundee.ac.uk, g.j.barton@dundee.ac.uk.

AB - Motivation: The current generation of DNA sequencing technologies produce a large amount of data quickly. All of these data need to pass some form of quality control (QC) processing and checking before they can be used for any analysis. The large number of samples that are run through Illumina sequencing machines makes the process of QC an onerous and time-consuming task that requires multiple pieces of information from several sources.Results: AlmostSignificant is an open-source platform for aggregating multiple sources of quality metrics as well as run and sample meta-data associated with DNA sequencing runs from Illumina sequencing machines. AlmostSignificant is a graphical platform to streamline the QC of DNA sequencing data, to store these data for future reference together with extra meta-data associated with the sequencing runs not typically retained. This simplifies the challenge of monitoring the volume of data produced by Illumina sequencers. AlmostSignificant has been used to track the quality of over 80 sequencing runs covering over 2500 samples produced over the last three years.Availability: The code and documentation for AlmostSignificant is freely available at https://github.com/bartongroup/AlmostSignificant CONTACT: c.cole@dundee.ac.uk, g.j.barton@dundee.ac.uk.

U2 - 10.1093/bioinformatics/btw559

DO - 10.1093/bioinformatics/btw559

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SP - 3850

EP - 3851

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

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ER -

AlmostSignificant: simplifying quality control of high-throughput sequencing data

Abstract

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AlmostSignificant: Simplifying quality control of high-throughput sequencing data

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Cole, Christian

Cite this