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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
Evaluating genome assemblies with HMM-Flagger.
Mobin Asri1, Jordan M Eizenga1, Prajna Hebbar1
1Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
HMM-Flagger, a novel tool, accurately detects structural errors in genome assemblies using read coverage. It identifies issues like false duplications and collapsed blocks, improving assembly quality and validating complex genomic regions.
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Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Genome assembly is crucial for understanding genetic variation and disease.
- Detecting structural errors in haplotype-resolved assemblies remains a challenge.
- Reference-free methods are needed to assess assembly accuracy without a gold standard.
Purpose of the Study:
- To develop and validate HMM-Flagger, a novel reference-free tool for detecting structural errors in genome assemblies.
- To assess the performance of HMM-Flagger using both simulated and real sequencing data.
- To evaluate improvements in genome assembly quality over time using HMM-Flagger.
Main Methods:
- HMM-Flagger models read coverage using a hidden Markov model (HMM) with a Gaussian autoregressive process.
- The tool classifies coverage anomalies into erroneous blocks, false duplications, or collapsed blocks.
- Performance was evaluated using synthetic misassemblies and real data from Pacific Biosciences HiFi and Oxford Nanopore Technologies.
Main Results:
- HMM-Flagger achieved F1 scores of 78.4% and 60.4% for synthetic errors with PacBio HiFi and Oxford Nanopore data, respectively.
- The tool identified large misassemblies, including false duplications and collapse events, in human satellite regions of HG002 assemblies.
- Application to Human Pangenome Reference Consortium (HPRC) assemblies showed a significant reduction in error rates from 0.94% (release 1) to 0.38% (release 2).
Conclusions:
- HMM-Flagger is an effective reference-free tool for identifying structural errors in haplotype-resolved genome assemblies.
- The tool's performance highlights advancements in long-read sequencing technologies and assembly pipelines.
- HMM-Flagger successfully validated complex genomic regions, such as NOTCH2NL assemblies, demonstrating its utility in assessing high-quality genome references.