{"entity": "researcher", "timestamp": "2026-10-11T06:11:44.584Z", "family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "affiliations": ["Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907"}}, "publications": [{"entity": "publication", "iuid": "ab9b4fd3312a411fa7600da6cc9fc651", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651"}}, "title": "Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling.", "authors": [{"family": "Wenson", "given": "Leonie", "initials": "L", "orcid": "0000-0002-1864-1258", "researcher": {"href": "https://publications.scilifelab.se/researcher/989e0534adbd426386cec5526c5e9668.json"}}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Erbilgin", "given": "Y\u00fccel", "initials": "Y"}, {"family": "Salman", "given": "Bar\u0131\u015f", "initials": "B", "orcid": "0000-0002-7657-8576", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb919f7fcc794c8898fe800056d42f38.json"}}, {"family": "Sundqvist", "given": "Anders", "initials": "A"}, {"family": "Schaal", "given": "Wesley", "initials": "W", "orcid": "0000-0001-6770-0878", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab184845a24f4effb22ec2b338ab8960.json"}}, {"family": "Sandbaumh\u00fcter", "given": "Friederike A", "initials": "FA"}, {"family": "Jansson", "given": "Erik T", "initials": "ET"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Davidsson", "given": "Anton", "initials": "A"}, {"family": "Stenerl\u00f6w", "given": "Bo", "initials": "B", "orcid": "0000-0001-8878-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/22437ff9315d43089232926973feb0d2.json"}}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA", "orcid": "0000-0002-0731-2715", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cdf2cd80f5b4f87adf6d936b6390ee8.json"}}, {"family": "Lindstr\u00f6m", "given": "Mikael", "initials": "M", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O", "orcid": "0000-0003-2883-1925", "researcher": {"href": "https://publications.scilifelab.se/researcher/68df823efa304c0b9962684ac1515808.json"}}], "type": "journal article", "published": "2025-08-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "7130"}, "abstract": "The ability to analyze whether DNA contains lesions is essential in identifying mutagenic substances. Currently, the detection of single-stranded DNA breaks (SSBs) lacks precision. To address this limitation, we develop a method for sequence-templated erroneous end-labelling sequencing (STEEL-seq), which enables the mapping of SSBs. The method requires a highly error-prone DNA polymerase, so we engineer a chimeric DNA polymerase, Sloppymerase, capable of replicating DNA in the absence of one nucleotide. Following the omission of a specific nucleotide (e.g., dATP) from the reaction mixture, Sloppymerase introduces mismatches directly downstream of SSBs at positions where deoxyadenosine should occur. This mismatch pattern, coupled with the retention of sequence information flanking these sites, ensures that the identified hits are bona fide SSBs. STEEL-seq is compatible with a variety of sequencing technologies, as demonstrated using Sanger, Illumina, PacBio, and Nanopore systems. Using STEEL-seq, we determine the SSB/base pair frequency in the human genome to range between 0.7 and 3.8 \u00d7 10-6 with an enrichment in active promoter regions.", "doi": "10.1038/s41467-025-62512-4", "pmid": "40759655", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12322144"}, {"db": "pii", "key": "10.1038/s41467-025-62512-4"}], "notes": [], "created": "2025-08-19T13:16:23.958Z", "modified": "2025-11-28T10:45:45.544Z"}, {"entity": "publication", "iuid": "d76167800eee45eead58fcbd6d6ab475", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d76167800eee45eead58fcbd6d6ab475.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d76167800eee45eead58fcbd6d6ab475"}}, "title": "Designing efficient randstrobes for sequence similarity analyses.", "authors": [{"family": "Karami", "given": "Moein", "initials": "M"}, {"family": "Soltani Mohammadi", "given": "Aryan", "initials": "A"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Ekim", "given": "Bar\u0131\u015f", "initials": "B"}, {"family": "Shen", "given": "Wei", "initials": "W", "orcid": "0000-0002-8099-8258", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cab9041fcf64f32aa6f0628daaa6352.json"}}, {"family": "Guo", "given": "Lidong", "initials": "L"}, {"family": "Xu", "given": "Mengyang", "initials": "M", "orcid": "0000-0002-4487-7088", "researcher": {"href": "https://publications.scilifelab.se/researcher/6192fd159fab41f4bedd7e0e5c9d90fe.json"}}, {"family": "Pibiri", "given": "Giulio Ermanno", "initials": "GE"}, {"family": "Patro", "given": "Rob", "initials": "R", "orcid": "0000-0001-8463-1675", "researcher": {"href": "https://publications.scilifelab.se/researcher/516efc2f4b2c47b384bca0954e576169.json"}}, {"family": "Sahlin", "given": "Kristoffer", "initials": "K", "orcid": "0000-0001-7378-2320", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7fcc3f1dbb448659ee971c81fc45651.json"}}], "type": "journal article", "published": "2024-03-29", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "40", "issue": "4", "issn-l": "1367-4803"}, "abstract": "Substrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis. However, k-mers are limited to exact matches between sequences leading to alternative constructs. We recently introduced a class of new constructs, strobemers, that can match across substitutions and smaller insertions and deletions. Randstrobes, the most sensitive strobemer proposed in Sahlin (Effective sequence similarity detection with strobemers. Genome Res 2021a;31:2080-94. https://doi.org/10.1101/gr.275648.121), has been used in several bioinformatics applications such as read classification, short-read mapping, and read overlap detection. Recently, we showed that the more pseudo-random the behavior of the construction (measured in entropy), the more efficient the seeds for sequence similarity analysis. The level of pseudo-randomness depends on the construction operators, but no study has investigated the efficacy.\n\nIn this study, we introduce novel construction methods, including a Binary Search Tree-based approach that improves time complexity over previous methods. To our knowledge, we are also the first to address biases in construction and design three metrics for measuring bias. Our evaluation shows that our methods have favorable speed and sampling uniformity compared to existing approaches. Lastly, guided by our results, we change the seed construction in strobealign, a short-read mapper, and find that the results change substantially. We suggest combining the two results to improve strobealign's accuracy for the shortest reads in our evaluated datasets. Our evaluation highlights sampling biases that can occur and provides guidance on which operators to use when implementing randstrobes.\n\nAll methods and evaluation benchmarks are available in a public Github repository at https://github.com/Moein-Karami/RandStrobes. The scripts for running the strobealign analysis are found at https://github.com/NBISweden/strobealign-evaluation.", "doi": "10.1093/bioinformatics/btae187", "pmid": "38579261", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11034988"}, {"db": "pii", "key": "7641534"}], "notes": [], "created": "2024-11-12T16:29:07.745Z", "modified": "2024-11-25T10:22:47.284Z"}, {"entity": "publication", "iuid": "2a63fab4f8d341be97dda6d47d09befb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a63fab4f8d341be97dda6d47d09befb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a63fab4f8d341be97dda6d47d09befb"}}, "title": "BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.", "authors": [{"family": "H\u00f6jer", "given": "Pontus", "initials": "P", "orcid": "0000-0001-8010-4755", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f901467fc54bb3a162e533248ebb70.json"}}, {"family": "Frick", "given": "Tobias", "initials": "T", "orcid": "0000-0002-3174-2096", "researcher": {"href": "https://publications.scilifelab.se/researcher/374b7074648048cdb0823281009f73ab.json"}}, {"family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "researcher": {"href": "https://publications.scilifelab.se/researcher/058b6ec6390a41929dc1288f71de63d4.json"}}, {"family": "Pourbozorgi", "given": "Parham", "initials": "P", "orcid": "0000-0002-5957-627X", "researcher": {"href": "https://publications.scilifelab.se/researcher/520886f23ef54f008bff773ebb86f7b1.json"}}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A", "orcid": "0000-0001-7837-8597", "researcher": {"href": "https://publications.scilifelab.se/researcher/67107191b3e4405697d0c110b1fa2735.json"}}], "type": "journal article", "published": "2023-11-06", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": null, "issue": null, "pages": null}, "abstract": "Linked-read sequencing promises a one-method approach for genome-wide insights including single nucleotide variants (SNVs), structural variants, and haplotyping. We introduce Barcode Linked Reads (BLR), an open-source haplotyping pipeline capable of handling millions of barcodes and data from multiple linked-read technologies including DBS, 10\u00d7 Genomics, TELL-seq and stLFR. Running BLR on DBS linked-reads yielded megabase-scale phasing with low (<0.2%) switch error rates. Of 13616 protein-coding genes phased in the GIAB benchmark set (v4.2.1), 98.6% matched the BLR phasing. In addition, large structural variants showed concordance with HPRC-HG002 reference assembly calls. Compared to diploid assembly with PacBio HiFi reads, BLR phasing was more continuous when considering switch errors. We further show that integrating long reads at low coverage (\u223c10\u00d7) can improve phasing contiguity and reduce switch errors in tandem repeats. When compared to Long Ranger on 10\u00d7 Genomics data, BLR showed an increase in phase block N50 with low switch-error rates. For TELL-Seq and stLFR linked reads, BLR generated longer or similar phase block lengths and low switch error rates compared to results presented in the original publications. In conclusion, BLR provides a flexible workflow for comprehensive haplotype analysis of linked reads from multiple platforms.", "doi": "10.1093/nar/gkad1010", "pmid": "37941142", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7369811"}], "notes": [], "created": "2023-11-22T16:12:00.786Z", "modified": "2024-03-14T11:35:08.948Z"}, {"entity": "publication", "iuid": "a9377e38c4fb4ae1920a4247903d1f42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9377e38c4fb4ae1920a4247903d1f42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9377e38c4fb4ae1920a4247903d1f42"}}, "title": "Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.", "authors": [{"family": "Ratz", "given": "Michael", "initials": "M", "orcid": "0000-0002-9795-8033", "researcher": {"href": "https://publications.scilifelab.se/researcher/a481899ca58a467499f56af4feb5457c.json"}}, {"family": "von Berlin", "given": "Leonie", "initials": "L", "orcid": "0000-0002-7790-0395", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c69f77dcc374d63b6717bef930206f9.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/161d8b5fb6734b33ad5f5590edbc0cff.json"}}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256", "volume": "25", "issue": "3", "pages": "285-294"}, "abstract": "The mammalian brain contains many specialized cells that develop from a thin sheet of neuroepithelial progenitor cells. Single-cell transcriptomics revealed hundreds of molecularly diverse cell types in the nervous system, but the lineage relationships between mature cell types and progenitor cells are not well understood. Here we show in vivo barcoding of early progenitors to simultaneously profile cell phenotypes and clonal relations in the mouse brain using single-cell and spatial transcriptomics. By reconstructing thousands of clones, we discovered fate-restricted progenitor cells in the mouse hippocampal neuroepithelium and show that microglia are derived from few primitive myeloid precursors that massively expand to generate widely dispersed progeny. We combined spatial transcriptomics with clonal barcoding and disentangled migration patterns of clonally related cells in densely labeled tissue sections. Our approach enables high-throughput dense reconstruction of cell phenotypes and clonal relations at the single-cell and tissue level in individual animals and provides an integrated approach for understanding tissue architecture.", "doi": "10.1038/s41593-022-01011-x", "pmid": "35210624", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Single cell": "Service", "NGI Spatial omics": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8904259"}, {"db": "pii", "key": "10.1038/s41593-022-01011-x"}], "notes": [], "created": "2022-02-25T08:59:35.886Z", "modified": "2024-01-16T13:48:37.372Z"}, {"entity": "publication", "iuid": "2327daa01a69409ebeaa040fe7f5fbd3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2327daa01a69409ebeaa040fe7f5fbd3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2327daa01a69409ebeaa040fe7f5fbd3"}}, "title": "Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.", "authors": [{"family": "Garcia", "given": "Maxime", "initials": "M", "orcid": "0000-0003-2827-9261", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cf9b1b223f04296adcb6bd091c548de.json"}}, {"family": "Juhos", "given": "Szilveszter", "initials": "S"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "D\u00edaz De St\u00e5hl", "given": "Teresita", "initials": "T"}, {"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1dc80e61f574293a190f2f3ef464988.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}], "type": "journal article", "published": "2020-01-29", "journal": {"volume": "9", "issn": "2046-1402", "issue": null, "pages": "63", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.", "doi": "10.12688/f1000research.16665.2", "pmid": "32269765", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Long-term Support WABI": "Technology development", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Clinical Genomics Stockholm": "Collaborative", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7111497"}], "notes": [], "created": "2020-04-23T08:58:58.026Z", "modified": "2024-01-16T13:48:43.022Z"}, {"entity": "publication", "iuid": "3f6c987638d84add91fc127d7dc6af75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f6c987638d84add91fc127d7dc6af75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f6c987638d84add91fc127d7dc6af75"}}, "title": "De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Che", "given": "Huiwen", "initials": "H"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Dahlberg", "given": "Johan", "initials": "J"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2018-10-09", "journal": {"volume": "9", "issn": "2073-4425", "issue": "10", "pages": "486", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we performed a de novo assembly of two Swedish genomes that revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual. Around 6 Mb of these novel sequences (NS) are shared with a Chinese personal genome. The NS are highly repetitive, have an elevated GC-content, and are primarily located in centromeric or telomeric regions. Up to 1 Mb of NS can be assigned to chromosome Y, and large segments are also missing from GRCh38 at chromosomes 14, 17, and 21. Inclusion of NS into the GRCh38 reference radically improves the alignment and variant calling from short-read whole-genome sequencing data at several genomic loci. A re-analysis of a Swedish population-scale sequencing project yields > 75,000 putative novel single nucleotide variants (SNVs) and removes > 10,000 false positive SNV calls per individual, some of which are located in protein coding regions. Our results highlight that the GRCh38 reference is not yet complete and demonstrate that personal genome assemblies from local populations can improve the analysis of short-read whole-genome sequencing data.", "doi": "10.3390/genes9100486", "pmid": "30304863", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "genes9100486"}, {"db": "pmc", "key": "PMC6210158"}], "notes": [], "created": "2018-11-20T14:44:03.808Z", "modified": "2024-01-16T13:48:45.362Z"}, {"entity": "publication", "iuid": "2b03da6064944f1ebd0e28e70959a962", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b03da6064944f1ebd0e28e70959a962.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b03da6064944f1ebd0e28e70959a962"}}, "title": "WhatsHap: fast and accurate read-based phasing", "authors": [{"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Patterson", "given": "Murray", "initials": "M", "orcid": "0000-0002-4329-0234", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f486e32763144cf8b000e7c9ac8e522.json"}}, {"family": "Garg", "given": "Shilpa", "initials": "S"}, {"family": "O Fischer", "given": "Sarah", "initials": "S"}, {"family": "Pisanti", "given": "Nadia", "initials": "N", "orcid": "0000-0003-3915-7665", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a14ed1f0c67470893bc46f1fe9b3222.json"}}, {"family": "Klau", "given": "Gunnar W", "initials": "GW", "orcid": "0000-0002-6340-0090", "researcher": {"href": "https://publications.scilifelab.se/researcher/730d9cbebb944751b9f21cc14493d88f.json"}}, {"family": "Sch\u00f6enhuth", "given": "Alexander", "initials": "A"}, {"family": "Marschall", "given": "Tobias", "initials": "T", "orcid": "0000-0002-9376-1030", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cee9b21391f41d39abf838f8102f0c7.json"}}], "type": "posted-content", "published": "2016-11-02", "journal": {"volume": null, "issn": null, "issue": null, "pages": null, "title": "bioRxiv", "issn-l": null}, "abstract": null, "doi": "10.1101/085050", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Long-term Support WABI": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:56:02.491Z", "modified": "2021-06-21T15:53:21.078Z"}]}