Jozef Sitarcik, Tomas Vinar, Brona Brejova, Werner Krampl, Jaroslav Budis, Jan Radvanszky, Maria Lucka. WarpSTR: determining tandem repeat lengths using raw nanopore signals. Bioinformatics, 39(6). 2023.

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Download from publisher: https://dx.doi.org/10.1093/bioinformatics/btad388

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Abstract:

MOTIVATION: Short tandem repeats (STRs) are regions of a genome containing 
many consecutive copies of the same short motif, possibly with small 
variations. Analysis of STRs has many clinical uses but is limited by 
technology mainly due to STRs surpassing the used read length. Nanopore 
sequencing, as one of long-read sequencing technologies, produces very long 
reads, thus offering more possibilities to study and analyze STRs. 
Basecalling of nanopore reads is however particularly unreliable in 
repeating regions, and therefore direct analysis from raw nanopore data is 
required. 

RESULTS: Here, we present WarpSTR, a novel method for characterizing both 
simple and complex tandem repeats directly from raw nanopore signals using 
a finite-state automaton and a search algorithm analogous to dynamic time 
warping. By applying this approach to determine the lengths of 241 STRs, we 
demonstrate that our approach decreases the mean absolute error of the STR 
length estimate compared to basecalling and STRique. 

AVAILABILITY AND IMPLEMENTATION: WarpSTR is freely available at 
https://github.com/fmfi-compbio/warpstr.

Last update: 09/09/2023