Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data

We show that BWA MEM -5SP generally outperformed all other tools across most environments in terms of inter-contig read pairs and binning quality, followed by BWA MEM default. Chromap and Minimap2, while less effective in these metrics, demonstrated the highest computational efficiency.

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Publication Details

Journal
Genome biology
Published
2026-01-30
DOI
https://doi.org/10.1186/s13059-026-03970-x
Primary Topic
Gut microbiota and health
Type
article
Field-Weighted Citation Impact
0.00

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article

Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data

Yuxuan Du, Wenxuan Zuo, Jiawei Huang, Fengzhu Sun et al.
Genome biology
Gut microbiota and health
article

Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data

Yuxuan Du, Wenxuan Zuo, Jiawei Huang, Fengzhu Sun, Yuqiu Wang
article en

Abstract

We show that BWA MEM -5SP generally outperformed all other tools across most environments in terms of inter-contig read pairs and binning quality, followed by BWA MEM default. Chromap and Minimap2, while less effective in these metrics, demonstrated the highest computational efficiency.

Genome biologyVol. 27(1)
QB3 (US), University of Southern California (US), The University of Texas at San Antonio (US)
National Science Foundation
Openalex Percentile: Top 73%
Gut microbiota and health
DOIOpen Access PDFOpenAlex
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