PT  - JOURNAL ARTICLE
AU  - David Heller
AU  - Martin Vingron
TI  - SVIM-asm: Structural variant detection from haploid and diploid genome assemblies
AID  - 10.1101/2020.10.27.356907
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.10.27.356907
4099  - http://biorxiv.org/content/early/2020/10/27/2020.10.27.356907.short
4100  - http://biorxiv.org/content/early/2020/10/27/2020.10.27.356907.full
AB  - 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 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.Contact vingron{at}molgen.mpg.deSupplementary information Supplementary data are available online.Competing Interest StatementThe authors have declared no competing interest.