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Title: Gap Resolution

Abstract

Gap Resolution is a software package that was developed to improve Newbler genome assemblies by automating the closure of sequence gaps caused by repetitive regions in the DNA. This is done by performing the follow steps:1) Identify and distribute the data for each gap in sub-projects. 2) Assemble the data associated with each sub-project using a secondary assembler, such as Newbler or PGA. 3) Determine if any gaps are closed after reassembly, and either design fakes (consensus of closed gap) for those that closed or lab experiments for those that require additional data. The software requires as input a genome assembly produce by the Newbler assembler provided by Roche and 454 data containing paired-end reads.

Authors:
; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
Contributing Org.:
Lawrence Berkeley National Laboratory
OSTI Identifier:
1353036
Report Number(s):
Gap Resolution; 005242WKSTN00
R&D Project: KP1501040; CR-2741
DOE Contract Number:
AC02-05CH11231
Resource Type:
Software
Software Revision:
00
Software Package Number:
005242
Software CPU:
WKSTN
Open Source:
Yes
Source Code Available:
Yes
Related Software:
Newbler Assembler,reter Primer3, Perl 5.8 interp
Country of Publication:
United States

Citation Formats

Labutti, Kurt, Foster, Brian, and Lapidus, Alla. Gap Resolution. Computer software. https://www.osti.gov//servlets/purl/1353036. Vers. 00. USDOE. 25 Apr. 2017. Web.
Labutti, Kurt, Foster, Brian, & Lapidus, Alla. (2017, April 25). Gap Resolution (Version 00) [Computer software]. https://www.osti.gov//servlets/purl/1353036.
Labutti, Kurt, Foster, Brian, and Lapidus, Alla. Gap Resolution. Computer software. Version 00. April 25, 2017. https://www.osti.gov//servlets/purl/1353036.
@misc{osti_1353036,
title = {Gap Resolution, Version 00},
author = {Labutti, Kurt and Foster, Brian and Lapidus, Alla},
abstractNote = {Gap Resolution is a software package that was developed to improve Newbler genome assemblies by automating the closure of sequence gaps caused by repetitive regions in the DNA. This is done by performing the follow steps:1) Identify and distribute the data for each gap in sub-projects. 2) Assemble the data associated with each sub-project using a secondary assembler, such as Newbler or PGA. 3) Determine if any gaps are closed after reassembly, and either design fakes (consensus of closed gap) for those that closed or lab experiments for those that require additional data. The software requires as input a genome assembly produce by the Newbler assembler provided by Roche and 454 data containing paired-end reads.},
url = {https://www.osti.gov//servlets/purl/1353036},
doi = {},
year = {Tue Apr 25 00:00:00 EDT 2017},
month = {Tue Apr 25 00:00:00 EDT 2017},
note =
}

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