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Related Experiment Video

Updated: Sep 28, 2025

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Long-read mapping to repetitive reference sequences using Winnowmap2.

Chirag Jain^1,2, Arang Rhie³, Nancy F Hansen⁴

¹Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India. chirag@iisc.ac.in.

|April 2, 2022

Summary

This summary is machine-generated.

A new long-read mapping method, Winnowmap2, improves genome analysis by accurately mapping reads in repetitive DNA sequences. This overcomes allelic bias, enhancing variant detection in previously inaccessible genomic regions.

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Last Updated: Sep 28, 2025

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Published on: February 24, 2015

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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Published on: February 18, 2022

Area of Science:

Genomics
Bioinformatics

Background:

Repetitive sequences like segmental duplications challenge genome analysis.
Existing long-read mappers exhibit allelic bias, leading to incorrect alignments and variant calls in repeats.

Purpose of the Study:

To develop a novel long-read mapping method to overcome allelic bias in repetitive genomic regions.
To improve the accuracy of variant calling within complex repeat arrays.

Main Methods:

Developed Winnowmap2, a long-read mapping tool utilizing minimal confidently alignable substrings.
Winnowmap2 computes read mappings via a collection of confident subalignments.

Main Results:

Winnowmap2 demonstrates increased tolerance to structural variation within repeats.
The method shows enhanced sensitivity for detecting paralog-specific variants.
Winnowmap2 effectively mitigates allelic bias in repetitive sequences.

Conclusions:

Winnowmap2 enables more accurate variant calls in previously inaccessible repetitive genomic regions.
The new mapping approach enhances the analysis of complex genomic structures.