Qmotif: determination of telomere content from whole-genome sequence data.
Ontology highlight
ABSTRACT: Motivation
Changes in telomere length have been observed in cancer and can be indicative of mechanisms involved in carcinogenesis. Most methods used to estimate telomere length require laboratory analysis of DNA samples. Here, we present qmotif, a fast and easy tool that determines telomeric repeat sequences content as an estimate of telomere length directly from whole-genome sequencing.Results
qmotif shows similar results to quantitative PCR, the standard method for high-throughput clinical telomere length quantification. qmotif output correlates strongly with the output of other tools for determining telomere sequence content, TelSeq and TelomereHunter, but can run in a fraction of the time-usually under a minute.Availability and implementation
qmotif is implemented in Java and source code is available at https://github.com/AdamaJava/adamajava, with instructions on how to build and use the application available from https://adamajava.readthedocs.io/en/latest/.Supplementary information
Supplementary data are available at Bioinformatics Advances online.
SUBMITTER: Holmes O
PROVIDER: S-EPMC9710677 | biostudies-literature | 2022
REPOSITORIES: biostudies-literature
Publications
qmotif: determination of telomere content from whole-genome sequence data.
Holmes Oliver O Nones Katia K Tang Yue Hang YH Loffler Kelly A KA Lee Michael M Patch Ann-Marie AM Dagg Rebecca A RA Lau Loretta M S LMS Leonard Conrad C Wood Scott S Xu Qinying Q Pickett Hilda A HA Reddel Roger R RR Barbour Andrew P AP Grimmond Sean M SM Waddell Nicola N Pearson John V JV
Bioinformatics advances 20220131 1
<h4>Motivation</h4>Changes in telomere length have been observed in cancer and can be indicative of mechanisms involved in carcinogenesis. Most methods used to estimate telomere length require laboratory analysis of DNA samples. Here, we present qmotif, a fast and easy tool that determines telomeric repeat sequences content as an estimate of telomere length directly from whole-genome sequencing.<h4>Results</h4>qmotif shows similar results to quantitative PCR, the standard method for high-through ...[more]
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