ArticlebioRxiv : the preprint server for biology2026
Evaluating genome assemblies with HMM-Flagger.
Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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12 authors.
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Abstract
HMM-Flagger is a reference-free tool for detecting structural errors in haplotype-resolved genome assemblies based upon the coverage of mapped reads. It models read coverage with a hidden Markov model augmented by a Gaussian autoregressive process, which enables classifying coverage anomalies as erroneous blocks, false duplications, or collapsed blocks. Trained and tested on synthetic misassemblies, it detected synthetic errors using Pacific Biosciences HiFi and Oxford Nanopore Technologies R10 data with F1 scores of 78.4% and 60.4% respectively. When applied to six HG002 assemblies it revealed multiple large misassemblies including false duplications and collapse events in human satellites. Applied to assemblies from the Human Pangenome Reference Consortium (HPRC), HMM-Flagger demonstrated substantial improvements from release 1 (0.94% error rate) to release 2 (0.38%), reflecting technological advances. HMM-Flagger also validated NOTCH2NL assemblies in HPRC release 2 and confirmed the correctness of three novel structural configurations.
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Registered trials
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