NDLI: TopoQual polishes circular consensus sequencing data and accurately predicts quality scores

Content Provider	Springer Nature : BioMed Central
Author	Weerakoon, Minindu Lee, Sangjin Mitchell, Emily Heaton, Haynes
Abstract	Background Pacific Biosciences (PacBio) circular consensus sequencing (CCS), also known as high fidelity (HiFi) technology, has revolutionized modern genomics by producing long (10 + kb) and highly accurate reads. This is achieved by sequencing circularized DNA molecules multiple times and combining them into a consensus sequence. Currently, the accuracy and quality value estimation provided by HiFi technology are more than sufficient for applications such as genome assembly and germline variant calling. However, there are limitations in the accuracy of the estimated quality scores when it comes to somatic variant calling on single reads. Results To address the challenge of inaccurate quality scores for somatic variant calling, we introduce TopoQual, a novel tool designed to enhance the accuracy of base quality predictions. TopoQual leverages techniques including partial order alignments (POA), topologically parallel bases, and deep learning algorithms to polish consensus sequences. Our results demonstrate that TopoQual corrects approximately 31.9% of errors in PacBio consensus sequences. Additionally, it validates base qualities up to q59, which corresponds to one error in 0.9 million bases. These improvements will significantly enhance the reliability of somatic variant calling using HiFi data. Conclusion TopoQual represents a significant advancement in genomics by improving the accuracy of base quality predictions for PacBio HiFi sequencing data. By correcting a substantial proportion of errors and achieving high base quality validation, TopoQual enables confident and accurate somatic variant calling. This tool not only addresses a critical limitation of current HiFi technology but also opens new possibilities for precise genomic analysis in various research and clinical applications.
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-06020-0.pdf
Ending Page	11
Page Count	11
Starting Page	1
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/s12859-024-06020-0
Journal	BMC Bioinformatics
Issue Number	1
Volume Number	26
Language	English
Publisher	BioMed Central
Publisher Date	2025-01-16
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Topoqual Deep consensus Pacbio Circular consensus sequencing High fidelity Somatic mutations Quality scores Error correcting Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

TopoQual polishes circular consensus sequencing data and accurately predicts quality scores

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FiNGS: high quality somatic mutations using filters for next generation sequencing

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HISEA: HIerarchical SEed Aligner for PacBio data

QualComp: a new lossy compressor for quality scores based on rate distortion theory

SequelTools: a suite of tools for working with PacBio Sequel raw sequence data

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TopoQual polishes circular consensus sequencing data and accurately predicts quality scores

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TopoQual polishes circular consensus sequencing data and accurately predicts quality scores