Related Experiment Video
Updated: Nov 24, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
SVIM-asm: structural variant detection from haploid and diploid genome assemblies
David Heller1, Martin Vingron1
1Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.
Motivation:
With the availability of new sequencing technologies, the generation of haplotype-resolved genome assemblies up to chromosome scale has become feasible. These assemblies capture the complete genetic information of both parental haplotypes, increase structural variant (SV) calling sensitivity and enable direct genotyping and phasing of SVs. Yet, existing SV callers are designed for haploid genome assemblies only, do not support genotyping or detect only a limited set of SV classes.
Results:
We introduce our method SVIM-asm for the detection and genotyping of six common classes of SVs from haploid and diploid genome assemblies. Compared against the only other existing SV caller for diploid assemblies, DipCall, SVIM-asm detects more SV classes and reached higher F1 scores for the detection of insertions and deletions on two recently published assemblies of the HG002 individual.
Availability And Implementation:
SVIM-asm has been implemented in Python and can be easily installed via bioconda. Its source code is available at github.com/eldariont/svim-asm.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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