Protocols

TIDDIT specifications

Information


Unique identifier OMICS_30260
Name TIDDIT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++, Python
Computer skills Advanced
Stability Stable
Requirements
numpy, scipy, cmake
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Anna Lindstrand

Publication for TIDDIT

TIDDIT citations

 (2)
library_books

AMYCNE: Confident copy number assessment using whole genome sequencing data

2018
PLoS One
PMCID: 5868770
PMID: 29579039
DOI: 10.1371/journal.pone.0189710

[…] e using the Burrows-Wheeler Algorithm (BWA; MEM-algorithm, version 0.7.4-r385) [] and resulted in 30X mean coverage of the samples (range 15-40X coverage). The coverage BED files were generated using TIDDIT (https://github.com/SciLifeLab/TIDDIT) with the bin size set to 100 bases. This study was approved by the regional ethics board in Stockholm. […]

call_split

High resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing

2018
PLoS One
PMCID: 5846771
PMID: 29529047
DOI: 10.1371/journal.pone.0193928
call_split See protocol

[…] remaining pairs were aligned to the hg19 human reference genome sequence using bwa 0.7.4-r385 [] and resulted in a 3x mapped coverage. The mapped reads were processed using locally developed software TIDDIT (https://github.com/vezzi/TIDDIT) [], publically available under General Public License version 3.0, implementing a sliding window analogue of a previously published procedure [].A list of dete […]

TIDDIT institution(s)
Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden, Science for Life Laboratory, Dept of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
TIDDIT funding source(s)
Supported by the Swedish Research Council [2012-1526]; the Marianne and Marcus Wallenberg foundation [2014.0084]; the Swedish Society for Medical Research [S14-0210]; the Stockholm County Council; the Harald and Greta Jeanssons Foundation; the Ulf Lundahl memory fund through the Swedish Brain Foundation; the Nilsson Ehle donations and the Erik Rönnberg Foundation.

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