ReDiT: Repeat Discrepancy Tagger--a shotgun assembly finishing aid.
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.


BACKGROUND
The ReDiT program is freely available at http://web.cgb.ki.se/redit
Tammi
Martti T
MT
Karolinska Institutet, Center for Genomics and Bioinformatics (CGB), Berzelius Väg 35, S-171 77 Stockholm, Sweden. martti.tammi@cgb.ki.se
Arner
Erik
E
Kindlund
Ellen
E
Andersson
Björn
B
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D004282:Documentation / Q000379:methods*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D016678:Genome; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface; D015443:Word Processing / Q000379:methods