HapEdit: An accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies

Jong Hyun Kim; Woo Cheol Kim; Lei M. Li; Sanghyun Park

doi:10.1093/nar/gkr354

HapEdit: An accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies

Jong Hyun Kim, Woo Cheol Kim, Lei M. Li, Sanghyun Park

College of Computing

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

Abstract

The massively parallel sequencing technologies have recently flourished and dramatically cut the cost to sequence personal human genomes. Haplotype assembly from personal genomes sequenced using the massively parallel sequencing technologies is becoming a cost-effective and promising tool for human disease study. Computational assembly of haplotypes has been proved to be very accurate, but obviously contains errors. Here we present a tool, HapEdit, to assess the accuracy of assembled haplotypes and edit them manually. Using this tool, a user can break erroneous haplotype segments into smaller segments, or concatenate haplotype segments if the concatenated haplotype segments are sufficiently supported. A user can also edit bases with low-quality scores. HapEdit displays haplotype assemblies so that a user can easily navigate and pinpoint a region of interest. As inputs, HapEdit currently takes reads from the Polonator, Illumina, SOLiD, 454 and Sanger sequencing technologies.

Original language	English
Pages (from-to)	W557-W561
Journal	Nucleic acids research
Volume	39
Issue number	SUPPL. 2
DOIs	https://doi.org/10.1093/nar/gkr354
Publication status	Published - 2011 Jul 1

Bibliographical note

Funding Information:
The National Research Foundation of Korea (2009-0083311 to J.H.K., W.K. and S.P.; 2011-0004382 to S.P.); The National Institutes of Health, USA (HG002790 to L.M.L.). Funding for open access charge: The National Research Foundation of Korea [2009-0083311].

All Science Journal Classification (ASJC) codes

Genetics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1093/nar/gkr354

Cite this

@article{47a1819c5d004f4baa0954c7198727cb,

title = "HapEdit: An accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies",

abstract = "The massively parallel sequencing technologies have recently flourished and dramatically cut the cost to sequence personal human genomes. Haplotype assembly from personal genomes sequenced using the massively parallel sequencing technologies is becoming a cost-effective and promising tool for human disease study. Computational assembly of haplotypes has been proved to be very accurate, but obviously contains errors. Here we present a tool, HapEdit, to assess the accuracy of assembled haplotypes and edit them manually. Using this tool, a user can break erroneous haplotype segments into smaller segments, or concatenate haplotype segments if the concatenated haplotype segments are sufficiently supported. A user can also edit bases with low-quality scores. HapEdit displays haplotype assemblies so that a user can easily navigate and pinpoint a region of interest. As inputs, HapEdit currently takes reads from the Polonator, Illumina, SOLiD, 454 and Sanger sequencing technologies.",

author = "Kim, {Jong Hyun} and Kim, {Woo Cheol} and Li, {Lei M.} and Sanghyun Park",

note = "Funding Information: The National Research Foundation of Korea (2009-0083311 to J.H.K., W.K. and S.P.; 2011-0004382 to S.P.); The National Institutes of Health, USA (HG002790 to L.M.L.). Funding for open access charge: The National Research Foundation of Korea [2009-0083311].",

year = "2011",

month = jul,

day = "1",

doi = "10.1093/nar/gkr354",

language = "English",

volume = "39",

pages = "W557--W561",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "SUPPL. 2",

}

TY - JOUR

T1 - HapEdit

T2 - An accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies

AU - Kim, Jong Hyun

AU - Kim, Woo Cheol

AU - Li, Lei M.

AU - Park, Sanghyun

N1 - Funding Information: The National Research Foundation of Korea (2009-0083311 to J.H.K., W.K. and S.P.; 2011-0004382 to S.P.); The National Institutes of Health, USA (HG002790 to L.M.L.). Funding for open access charge: The National Research Foundation of Korea [2009-0083311].

PY - 2011/7/1

Y1 - 2011/7/1

N2 - The massively parallel sequencing technologies have recently flourished and dramatically cut the cost to sequence personal human genomes. Haplotype assembly from personal genomes sequenced using the massively parallel sequencing technologies is becoming a cost-effective and promising tool for human disease study. Computational assembly of haplotypes has been proved to be very accurate, but obviously contains errors. Here we present a tool, HapEdit, to assess the accuracy of assembled haplotypes and edit them manually. Using this tool, a user can break erroneous haplotype segments into smaller segments, or concatenate haplotype segments if the concatenated haplotype segments are sufficiently supported. A user can also edit bases with low-quality scores. HapEdit displays haplotype assemblies so that a user can easily navigate and pinpoint a region of interest. As inputs, HapEdit currently takes reads from the Polonator, Illumina, SOLiD, 454 and Sanger sequencing technologies.

AB - The massively parallel sequencing technologies have recently flourished and dramatically cut the cost to sequence personal human genomes. Haplotype assembly from personal genomes sequenced using the massively parallel sequencing technologies is becoming a cost-effective and promising tool for human disease study. Computational assembly of haplotypes has been proved to be very accurate, but obviously contains errors. Here we present a tool, HapEdit, to assess the accuracy of assembled haplotypes and edit them manually. Using this tool, a user can break erroneous haplotype segments into smaller segments, or concatenate haplotype segments if the concatenated haplotype segments are sufficiently supported. A user can also edit bases with low-quality scores. HapEdit displays haplotype assemblies so that a user can easily navigate and pinpoint a region of interest. As inputs, HapEdit currently takes reads from the Polonator, Illumina, SOLiD, 454 and Sanger sequencing technologies.

UR - http://www.scopus.com/inward/record.url?scp=79960002429&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79960002429&partnerID=8YFLogxK

U2 - 10.1093/nar/gkr354

DO - 10.1093/nar/gkr354

M3 - Article

C2 - 21576217

AN - SCOPUS:79960002429

SN - 0305-1048

VL - 39

SP - W557-W561

JO - Nucleic acids research

JF - Nucleic acids research

IS - SUPPL. 2

ER -

HapEdit: An accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this