YaHS: yet another Hi-C scaffolding tool

Abstract Summary We present YaHS, a user-friendly command-line tool for the construction of chromosome-scale scaffolds from Hi-C data. It can be run with a single-line command, requires minimal input from users (an assembly file and an alignment file) which is compatible with similar tools and provi...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) Vol. 39; no. 1
Main Authors: Zhou, Chenxi, McCarthy, Shane A, Durbin, Richard
Format: Journal Article
Language:English
Published: England Oxford University Press 01.01.2023
Oxford Publishing Limited (England)
Subjects:
Assembly
Availability
Bioinformatics
Documentation
Scaffolding
Software
Source code
User requirements
ISSN:1367-4803, 1367-4811, 1367-4811
Online Access:Get full text
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Description
Summary:Abstract Summary We present YaHS, a user-friendly command-line tool for the construction of chromosome-scale scaffolds from Hi-C data. It can be run with a single-line command, requires minimal input from users (an assembly file and an alignment file) which is compatible with similar tools and provides assembly results in multiple formats, thereby enabling rapid, robust and scalable construction of high-quality genome assemblies with high accuracy and contiguity. Availability and implementation YaHS is implemented in C and licensed under the MIT License. The source code, documentation and tutorial are available at https://github.com/sanger-tol/yahs. Supplementary information Supplementary data are available at Bioinformatics online.
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ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btac808