ReDiT: Repeat Discrepancy Tagger—a shotgun assembly finishing aid | Zendy

Martti T. Tammi | Zendy; Peter Arner | Zendy; Ellen Kindlund | Zendy; Björn Andersson | Zendy

AI Assistant Blog Pricing

Home ZAIA Blog

Open Access

ReDiT: Repeat Discrepancy Tagger—a shotgun assembly finishing aid

Author(s) -

Martti T. Tammi,

Peter Arner,

Ellen Kindlund,

Björn Andersson

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bth004

Subject(s) - shotgun sequencing , shotgun , computer science , sequence assembly , software , fragment (logic) , closure (psychology) , sequence (biology) , programming language , dna sequencing , genetics , biology , dna , gene , gene expression , transcriptome , economics , market economy

Finishing, i.e. gap closure and editing, is the most time-consuming part of genome sequencing. Repeated sequences together with sequencing errors complicate the assembly and often result in misassemblies that are difficult to correct. Repeat Discrepancy Tagger (ReDiT) is a tool designed to aid in the finishing step. This software processes assembly results produced by any fragment assembly program that outputs ace files. The input sequences are analyzed to determine possible differences between repeated sequences. The output is written as tags in an ace file that can be viewed by, e.g. the Consed sequence editor.

The content you want is available to Zendy users.

Already have an account? Click here to sign in.

Having issues? You can contact us here

Accelerating Research