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qmotif: determination of telomere content from whole-genome sequence data.

Authors :: Holmes O
Nones K
Tang YH
Loffler KA
Lee M
Patch AM
Dagg RA
Lau LMS
Leonard C
Wood S
Xu Q
Pickett HA
Reddel RR
Barbour AP
Grimmond SM
Waddell N
Pearson JV
Source :: Bioinformatics advances [Bioinform Adv] 2022 Jan 31; Vol. 2 (1), pp. vbac005. Date of Electronic Publication: 2022 Jan 31 (Print Publication: 2022).
Publication Year :: 2022
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.<br />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.<br />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/.<br />Supplementary Information: Supplementary data are available at Bioinformatics Advances online.<br /> (© The Author(s) 2022. Published by Oxford University Press.)