TRhist specifications

Information


Unique identifier OMICS_00117
Name TRhist
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output data The repeat unit, length of the short tandem repeat (STR), number of mutations in the STR, flanking regions surrounding the STR and other paired-end read.
Output format CSV, FASTA
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.0.1
Stability Stable
Requirements
JRE
Source code URL https://trhist.gi.k.u-tokyo.ac.jp/ver1.0.1/TRhist_src.zip
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Shinichi Morishita

Additional information


http://trhist.gi.k.u-tokyo.ac.jp/ver1.0.1/TRhistManual.txt

Publication for TRhist

TRhist citation

library_books

Interrogating the “unsequenceable” genomic trinucleotide repeat disorders by long read sequencing

2017
Genome Med
PMCID: 5514472
PMID: 28720120
DOI: 10.1186/s13073-017-0456-7

[…] licon sequencing and whole-genome sequencing (WGS). It is worth noting that RepeatHMM is different from several previously published tools, such as RepeatMasker [], tandem repeat finder (TRF) [], and TRhist [], which screen for simple/intersperse repeats only for a query sequence. RepeatHMM is also different from lobSTR [], which infers microsatellites from short-read sequencing data, or PacmonsTR […]

TRhist institution(s)
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Department of Information and Communication Engineering, Faculty of Engineering and Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
TRhist funding source(s)
Supported by Grant-in-Aid for Scientific Research on Innovative Areas (22129008, 221S0002) (in part) from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and by the Global COE program (Deciphering Biosphere from Genome Big Bang) from the MEXT.

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