A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq)

Hanan Begali

doi:doi:10.11648/j.ejb.20180601.12

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A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq)

Hanan Begali

Published in European Journal of Biophysics (Volume 6, Issue 1)

Received: 19 October 2017 Accepted: 27 December 2017 Published: 20 January 2018

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Abstract

Motivation: The discovery and assessment genetic variants for Next Generation Sequencing (NGS), including Restriction site Associated DNA sequencing (RADSeq), is an important task in bioinformatics and comparative genetics. The genetic variants can be single-nucleotide polymorphisms (SNPs), insertions and deletions (Indels) when compared to a reference genome. Usually, the short reads are aligned to a reference genome at first using NGS alignment software, such as the Burrows- Wheeler Aligner (BWA). The alignment is usually stored into a BAM file, a binary format of standard SAM (Sequence Alignment/Map) protocol. Then analysis software, such as Genome analysis Toolkit (GATK) or SAMTools [30] [31], together with scripts written in R programming language, could provide an efficient solution for calling variants. We focused on RADSeq-based marker selection for Arabidopsis thaliana. RADSeq consists short reads that do not cover the whole reference genome. Finally, SNPs as output in Variant Call Format (VCF) have been visualized by Integrative Genomics Viewer (IGV) software. We found that the visualization of SNPs and Indels is helpful and provides us with valuable insights on marker selection. We found that applying Chi-Square test for all target genotypes, which are homozygous reference 0/0, heterozygous variants 0/1 and homozygous variants 1/1, to test Hardy-Weinberg Equilibrium (HWE) in order to reduce false positive rate significantly and we showed that our pipeline is efficient in RADSeq-based marker selection.

Published in	European Journal of Biophysics (Volume 6, Issue 1)
DOI	10.11648/j.ejb.20180601.12
Page(s)	7-16
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2018. Published by Science Publishing Group

Keywords

NGS-RADSeq, Arabidopsis thaliana (TAIR10), GATK, SAMTools, Chi-Square Test, HWE-P, Reliable SNPs

References

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Hanan Begali. (2018). A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq). European Journal of Biophysics, 6(1), 7-16. https://doi.org/10.11648/j.ejb.20180601.12

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Hanan Begali. A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq). Eur. J. Biophys. 2018, 6(1), 7-16. doi: 10.11648/j.ejb.20180601.12

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Hanan Begali. A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq). Eur J Biophys. 2018;6(1):7-16. doi: 10.11648/j.ejb.20180601.12

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@article{10.11648/j.ejb.20180601.12,
  author = {Hanan Begali},
  title = {A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq)},
  journal = {European Journal of Biophysics},
  volume = {6},
  number = {1},
  pages = {7-16},
  doi = {10.11648/j.ejb.20180601.12},
  url = {https://doi.org/10.11648/j.ejb.20180601.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ejb.20180601.12},
  abstract = {Motivation: The discovery and assessment genetic variants for Next Generation Sequencing (NGS), including Restriction site Associated DNA sequencing (RADSeq), is an important task in bioinformatics and comparative genetics. The genetic variants can be single-nucleotide polymorphisms (SNPs), insertions and deletions (Indels) when compared to a reference genome. Usually, the short reads are aligned to a reference genome at first using NGS alignment software, such as the Burrows- Wheeler Aligner (BWA). The alignment is usually stored into a BAM file, a binary format of standard SAM (Sequence Alignment/Map) protocol. Then analysis software, such as Genome analysis Toolkit (GATK) or SAMTools [30] [31], together with scripts written in R programming language, could provide an efficient solution for calling variants. We focused on RADSeq-based marker selection for Arabidopsis thaliana. RADSeq consists short reads that do not cover the whole reference genome. Finally, SNPs as output in Variant Call Format (VCF) have been visualized by Integrative Genomics Viewer (IGV) software. We found that the visualization of SNPs and Indels is helpful and provides us with valuable insights on marker selection. We found that applying Chi-Square test for all target genotypes, which are homozygous reference 0/0, heterozygous variants 0/1 and homozygous variants 1/1, to test Hardy-Weinberg Equilibrium (HWE) in order to reduce false positive rate significantly and we showed that our pipeline is efficient in RADSeq-based marker selection.},
 year = {2018}
}

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TY  - JOUR
T1  - A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq)
AU  - Hanan Begali
Y1  - 2018/01/20
PY  - 2018
N1  - https://doi.org/10.11648/j.ejb.20180601.12
DO  - 10.11648/j.ejb.20180601.12
T2  - European Journal of Biophysics
JF  - European Journal of Biophysics
JO  - European Journal of Biophysics
SP  - 7
EP  - 16
PB  - Science Publishing Group
SN  - 2329-1737
UR  - https://doi.org/10.11648/j.ejb.20180601.12
AB  - Motivation: The discovery and assessment genetic variants for Next Generation Sequencing (NGS), including Restriction site Associated DNA sequencing (RADSeq), is an important task in bioinformatics and comparative genetics. The genetic variants can be single-nucleotide polymorphisms (SNPs), insertions and deletions (Indels) when compared to a reference genome. Usually, the short reads are aligned to a reference genome at first using NGS alignment software, such as the Burrows- Wheeler Aligner (BWA). The alignment is usually stored into a BAM file, a binary format of standard SAM (Sequence Alignment/Map) protocol. Then analysis software, such as Genome analysis Toolkit (GATK) or SAMTools [30] [31], together with scripts written in R programming language, could provide an efficient solution for calling variants. We focused on RADSeq-based marker selection for Arabidopsis thaliana. RADSeq consists short reads that do not cover the whole reference genome. Finally, SNPs as output in Variant Call Format (VCF) have been visualized by Integrative Genomics Viewer (IGV) software. We found that the visualization of SNPs and Indels is helpful and provides us with valuable insights on marker selection. We found that applying Chi-Square test for all target genotypes, which are homozygous reference 0/0, heterozygous variants 0/1 and homozygous variants 1/1, to test Hardy-Weinberg Equilibrium (HWE) in order to reduce false positive rate significantly and we showed that our pipeline is efficient in RADSeq-based marker selection.
VL  - 6
IS  - 1
ER  -

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Author Information

Hanan Begali

Department of Life Science Informatics Master Program, Bonn-Aachen International Center for Information Technology B-IT at Bonn University, Bonn, Germany

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Hanan Begali. (2018). A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq). European Journal of Biophysics, 6(1), 7-16. https://doi.org/10.11648/j.ejb.20180601.12

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Hanan Begali. A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq). Eur. J. Biophys. 2018, 6(1), 7-16. doi: 10.11648/j.ejb.20180601.12

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Hanan Begali. A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq). Eur J Biophys. 2018;6(1):7-16. doi: 10.11648/j.ejb.20180601.12

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@article{10.11648/j.ejb.20180601.12,
  author = {Hanan Begali},
  title = {A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq)},
  journal = {European Journal of Biophysics},
  volume = {6},
  number = {1},
  pages = {7-16},
  doi = {10.11648/j.ejb.20180601.12},
  url = {https://doi.org/10.11648/j.ejb.20180601.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ejb.20180601.12},
  abstract = {Motivation: The discovery and assessment genetic variants for Next Generation Sequencing (NGS), including Restriction site Associated DNA sequencing (RADSeq), is an important task in bioinformatics and comparative genetics. The genetic variants can be single-nucleotide polymorphisms (SNPs), insertions and deletions (Indels) when compared to a reference genome. Usually, the short reads are aligned to a reference genome at first using NGS alignment software, such as the Burrows- Wheeler Aligner (BWA). The alignment is usually stored into a BAM file, a binary format of standard SAM (Sequence Alignment/Map) protocol. Then analysis software, such as Genome analysis Toolkit (GATK) or SAMTools [30] [31], together with scripts written in R programming language, could provide an efficient solution for calling variants. We focused on RADSeq-based marker selection for Arabidopsis thaliana. RADSeq consists short reads that do not cover the whole reference genome. Finally, SNPs as output in Variant Call Format (VCF) have been visualized by Integrative Genomics Viewer (IGV) software. We found that the visualization of SNPs and Indels is helpful and provides us with valuable insights on marker selection. We found that applying Chi-Square test for all target genotypes, which are homozygous reference 0/0, heterozygous variants 0/1 and homozygous variants 1/1, to test Hardy-Weinberg Equilibrium (HWE) in order to reduce false positive rate significantly and we showed that our pipeline is efficient in RADSeq-based marker selection.},
 year = {2018}
}

Copy | Download

TY  - JOUR
T1  - A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (RADSeq)
AU  - Hanan Begali
Y1  - 2018/01/20
PY  - 2018
N1  - https://doi.org/10.11648/j.ejb.20180601.12
DO  - 10.11648/j.ejb.20180601.12
T2  - European Journal of Biophysics
JF  - European Journal of Biophysics
JO  - European Journal of Biophysics
SP  - 7
EP  - 16
PB  - Science Publishing Group
SN  - 2329-1737
UR  - https://doi.org/10.11648/j.ejb.20180601.12
AB  - Motivation: The discovery and assessment genetic variants for Next Generation Sequencing (NGS), including Restriction site Associated DNA sequencing (RADSeq), is an important task in bioinformatics and comparative genetics. The genetic variants can be single-nucleotide polymorphisms (SNPs), insertions and deletions (Indels) when compared to a reference genome. Usually, the short reads are aligned to a reference genome at first using NGS alignment software, such as the Burrows- Wheeler Aligner (BWA). The alignment is usually stored into a BAM file, a binary format of standard SAM (Sequence Alignment/Map) protocol. Then analysis software, such as Genome analysis Toolkit (GATK) or SAMTools [30] [31], together with scripts written in R programming language, could provide an efficient solution for calling variants. We focused on RADSeq-based marker selection for Arabidopsis thaliana. RADSeq consists short reads that do not cover the whole reference genome. Finally, SNPs as output in Variant Call Format (VCF) have been visualized by Integrative Genomics Viewer (IGV) software. We found that the visualization of SNPs and Indels is helpful and provides us with valuable insights on marker selection. We found that applying Chi-Square test for all target genotypes, which are homozygous reference 0/0, heterozygous variants 0/1 and homozygous variants 1/1, to test Hardy-Weinberg Equilibrium (HWE) in order to reduce false positive rate significantly and we showed that our pipeline is efficient in RADSeq-based marker selection.
VL  - 6
IS  - 1
ER  -

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