BAIT: Organizing genomes and mapping rearrangements in single cells

Strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (SCEs) and other rearrangements. To analyze these data, we introduce BAIT, software which assigns templates and identifies and localizes SCEs. We demonstrate BAIT can refine completed reference assemblies, iden...

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Autores principales: Hills, Mark, O’Neill, Kieran, Falconer, Ester, Brinkman, Ryan, Lansdorp, Peter M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971352/
https://www.ncbi.nlm.nih.gov/pubmed/24028793
http://dx.doi.org/10.1186/gm486
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author Hills, Mark
O’Neill, Kieran
Falconer, Ester
Brinkman, Ryan
Lansdorp, Peter M
author_facet Hills, Mark
O’Neill, Kieran
Falconer, Ester
Brinkman, Ryan
Lansdorp, Peter M
author_sort Hills, Mark
collection PubMed
description Strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (SCEs) and other rearrangements. To analyze these data, we introduce BAIT, software which assigns templates and identifies and localizes SCEs. We demonstrate BAIT can refine completed reference assemblies, identifying approximately 21 Mb of incorrectly oriented fragments and placing over half (2.6 Mb) of the orphan fragments in mm10/GRCm38. BAIT also stratifies scaffold-stage assemblies, potentially accelerating the assembling and finishing of reference genomes. BAIT is available at http://sourceforge.net/projects/bait/.
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spelling pubmed-39713522014-04-02 BAIT: Organizing genomes and mapping rearrangements in single cells Hills, Mark O’Neill, Kieran Falconer, Ester Brinkman, Ryan Lansdorp, Peter M Genome Med Software Strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (SCEs) and other rearrangements. To analyze these data, we introduce BAIT, software which assigns templates and identifies and localizes SCEs. We demonstrate BAIT can refine completed reference assemblies, identifying approximately 21 Mb of incorrectly oriented fragments and placing over half (2.6 Mb) of the orphan fragments in mm10/GRCm38. BAIT also stratifies scaffold-stage assemblies, potentially accelerating the assembling and finishing of reference genomes. BAIT is available at http://sourceforge.net/projects/bait/. BioMed Central 2013-09-13 /pmc/articles/PMC3971352/ /pubmed/24028793 http://dx.doi.org/10.1186/gm486 Text en Copyright © 2013 Hills et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Hills, Mark
O’Neill, Kieran
Falconer, Ester
Brinkman, Ryan
Lansdorp, Peter M
BAIT: Organizing genomes and mapping rearrangements in single cells
title BAIT: Organizing genomes and mapping rearrangements in single cells
title_full BAIT: Organizing genomes and mapping rearrangements in single cells
title_fullStr BAIT: Organizing genomes and mapping rearrangements in single cells
title_full_unstemmed BAIT: Organizing genomes and mapping rearrangements in single cells
title_short BAIT: Organizing genomes and mapping rearrangements in single cells
title_sort bait: organizing genomes and mapping rearrangements in single cells
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971352/
https://www.ncbi.nlm.nih.gov/pubmed/24028793
http://dx.doi.org/10.1186/gm486
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