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Genome Annotation and Assembly

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Related Experiment Video

Updated: Jun 11, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs.

Ivan Tolstoganov¹, Zhoutao Chen², Pavel Pevzner³

¹Department of Mathematics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.

|October 1, 2024

Summary

SpLitteR tool enhances diploid genome assembly using linked-reads, improving contiguity and accuracy. It effectively bridges repeats in phased assemblies, outperforming existing methods for better genome reconstruction.

Keywords:

Assembly graph Repeat resolution Tell-seq

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Last Updated: Jun 11, 2025

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Long-read sequencing (e.g., high-fidelity or HiFi) enables contiguous genome assemblies but struggles with repeats longer than read lengths.
Diploid genome assembly is challenged by shared long identical regions between haplomes, limiting contiguity.
Existing methods often require additional experimental technologies to improve diploid assembly contiguity.

Purpose of the Study:

To develop a novel tool, SpLitteR, for improving diploid genome assembly using linked-reads and assembly graphs.
To evaluate the effectiveness of SpLitteR in phasing and scaffolding assembly graphs.
To assess SpLitteR's performance against state-of-the-art linked-read scaffolders.

Main Methods:

Development of the SpLitteR tool for assembly graph phasing and scaffolding.
Utilization of barcoded linked-reads generated by TELL-Seq technology.
Benchmarking SpLitteR against ARKS and SLR-superscaffolder using human HG002 genome and sheep gut microbiome datasets.

Main Results:

SpLitteR achieved a 1.5-fold increase in NGA50 compared to baseline LJA assembly and other scaffolders on the human HG002 dataset.
SpLitteR introduced no additional misassemblies in the human genome dataset.
TELL-Seq reads were shown to facilitate phasing and scaffolding within assembly graphs.

Conclusions:

SpLitteR effectively improves the accuracy and contiguity of diploid genome assemblies.
The tool leverages linked-reads to bridge unresolved repeats, enhancing genome reconstruction.
SpLitteR is available as part of the SPAdes package, offering an accessible solution for advanced genome assembly.