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Updated: Jun 13, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Fast and Accurate Draft Genome Patching with GPatch.

Adam Diehl¹, Alan Boyle^1,2

¹Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA, 48109.

Biorxiv : the Preprint Server for Biology

|June 12, 2025

Summary

This summary is machine-generated.

GPatch creates accurate, gap-free chromosome-scale pseudoassemblies from fragmented draft genomes. This tool enhances genomic variation studies and enables Hi-C data analysis, maximizing the utility of draft genome sequences.

Keywords:

Computational genomics Functional genomics Genome assembly Genomic mapping Genomic variations Hi-C data analysis Intraspecific variation Long-read sequencing Reference genome Reference-guided patching Sequence alignment Structural variation

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Area of Science:

Genomics
Bioinformatics

Background:

Advancements in sequencing technologies have produced many long-read draft genomes.
Draft genomes are fragmented, limiting their use in functional genomics.

Purpose of the Study:

To introduce GPatch, a novel tool for constructing chromosome-scale pseudoassemblies from fragmented draft genomes.
To improve the usability of draft genomes for downstream analyses like Hi-C data.

Main Methods:

GPatch utilizes alignments to a reference genome to build pseudoassemblies.
The tool reconstructs complete, accurate, and gap-free genome sequences.

Main Results:

GPatch preserves over 95% of nucleotides from original draft genomes.
GPatch assemblies are suitable for Hi-C data analysis, unlike draft assemblies.
The tool generates chromosome-scale pseudoassemblies.

Conclusions:

GPatch is essential for maximizing the utility of draft genomes until complete genome assembly is standard.
The tool overcomes fragmentation challenges in draft genomes for functional genomics.