{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T20:26:01Z","timestamp":1776457561320,"version":"3.51.2"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"22-23","license":[{"start":{"date-parts":[[2020,12,21]],"date-time":"2020-12-21T00:00:00Z","timestamp":1608508800000},"content-version":"vor","delay-in-days":20,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"German Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"crossref","award":["031L0169A"],"award-info":[{"award-number":["031L0169A"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]},{"name":"International Max Planck Research School for Biology and Computation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1034","type":"journal-article","created":{"date-parts":[[2020,12,9]],"date-time":"2020-12-09T00:04:36Z","timestamp":1607472276000},"page":"5519-5521","source":"Crossref","is-referenced-by-count":143,"title":["SVIM-asm: structural variant detection from haploid and diploid genome assemblies"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8346-9565","authenticated-orcid":false,"given":"David","family":"Heller","sequence":"first","affiliation":[{"name":"Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics , Berlin 14195, Germany"}]},{"given":"Martin","family":"Vingron","sequence":"additional","affiliation":[{"name":"Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics , Berlin 14195, Germany"}]}],"member":"286","published-online":{"date-parts":[[2020,12,21]]},"reference":[{"key":"2023062707203611200_btaa1034-B1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","year":"2015","journal-title":"Nature"},{"key":"2023062707203611200_btaa1034-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-018-08148-z","article-title":"Multi-platform discovery of haplotype-resolved structural variation in human genomes","volume":"10","author":"Chaisson","year":"2019","journal-title":"Nat. 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Biotechnol","author":"Garg","year":"2020"},{"key":"2023062707203611200_btaa1034-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-019-1911-0","article-title":"SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies","volume":"20","author":"Goel","year":"2019","journal-title":"Genome Biol"},{"key":"2023062707203611200_btaa1034-B5","doi-asserted-by":"crossref","first-page":"2907","DOI":"10.1093\/bioinformatics\/btz041","article-title":"SVIM: structural variant identification using mapped long reads","volume":"35","author":"Heller","year":"2019","journal-title":"Bioinformatics"},{"key":"2023062707203611200_btaa1034-B6","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1186\/s13059-019-1720-5","article-title":"Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing","volume":"20","author":"Kosugi","year":"2019","journal-title":"Genome Biol"},{"key":"2023062707203611200_btaa1034-B7","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2023062707203611200_btaa1034-B8","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/s41592-018-0054-7","article-title":"A synthetic-diploid benchmark for accurate variant-calling evaluation","volume":"15","author":"Li","year":"2018","journal-title":"Nat. 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