MANASIG: Python Package to MAnipulateNAnopore SIGnals from sequencing files

článek ve sborníku ve WoS nebo Scopus

angličtina

Sequencing technology allows us to study the structure and function of several genomic processes. Recently, nanopore sequencing technology has become widely used. It allows us to study a single molecule's structure and provide reads several times longer than previously used second sequencer generation methods. However, the error rate is still higher, which limits further analysis. The main source of errors is in the base-calling process. Nanopore sequencers produce a digital signal based on the electric potential's alternations on the pore. The signal then needs to be translated to the sequence of characters representing the nucleotides. The Base-calling process is still improving, but there is a potential to bypass it and process the raw signal data as the carrier of the sequenced molecule information. Thus we present a Python package designed to manipulate, extract and process nanopore sequencing files and provide a helpful tool to analyze squiggles. It provides a single API to access the reads attributes allowing extraction and signal visualization. The package can work with base-called data and provide a known BLAST search process to select specific regions of interest. The package is available at: https://github.com/VojtechBarton/manasig

Python package, Nanopore sequencing, Signal processing

BARTOŇ, V.; NYKRÝNOVÁ, M.; ŠKUTKOVÁ, H.

9. 12. 2021

978-1-6654-0126-5

2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

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