{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T17:05:52Z","timestamp":1775840752267,"version":"3.50.1"},"reference-count":27,"publisher":"Microbiology Society","issue":"4","license":[{"start":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T00:00:00Z","timestamp":1775779200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018336","name":"National Institute for Health Research Health Protection Research Unit","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100018336","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["226007\/Z\/22\/Z"],"award-info":[{"award-number":["226007\/Z\/22\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Institute of Health","award":["1R01AI146338"],"award-info":[{"award-number":["1R01AI146338"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,10]]},"abstract":"<jats:p>\n                    Whole-genome sequencing provides a vast amount of genetic information, but its use in clinical and epidemiological studies often depends on the accurate inference of genomic variants. Comparative genomic studies in\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    typically involve mapping short reads from a diverse population to the same reference genome. This approach can lead to the incorrect characterization of many genomic regions that are susceptible to mapping bias when the reference is too distantly related to the sample. We analysed the consequences of mapping reads from different lineages of\n                    <jats:italic>M. tuberculosis<\/jats:italic>\n                    to the commonly used reference H37Rv and showed that the mapping bias varied depending on both the lineage and the gene mapped. To resolve these issues, we propose a new hybrid workflow which involves three steps: first, building a\n                    <jats:italic>de novo<\/jats:italic>\n                    assembly from short reads; second, aligning this assembly to a reference genome; and finally, mapping the reads to this aligned assembly. We show that many of the lineage and gene biases were corrected using this approach, which leads to a better characterization of lineages and hypervariable regions in comparative analysis. Our proposed approach will enable researchers to elucidate more genetic variations in\n                    <jats:italic>M. tuberculosis<\/jats:italic>\n                    and other bacterial pathogens.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001690","type":"journal-article","created":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T16:16:46Z","timestamp":1775837806000},"source":"Crossref","is-referenced-by-count":0,"title":["Reducing mapping reference and lineage bias in Mycobacterium tuberculosis"],"prefix":"10.1099","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2492-0958","authenticated-orcid":false,"given":"Arturo","family":"Torres Ortiz","sequence":"first","affiliation":[{"name":"Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA"},{"name":"Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1885-500X","authenticated-orcid":false,"given":"Xavier","family":"Didelot","sequence":"additional","affiliation":[{"name":"School of Life Sciences and Department of Statistics, University of Warwick, Coventry, CV4 7AL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1457-8327","authenticated-orcid":false,"given":"Louis","family":"Grandjean","sequence":"additional","affiliation":[{"name":"Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3226"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1800474"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-019-0214-5"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2017.10.030"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1038\/31159"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2016.03.007"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0030593"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000418"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1038\/nrg.2016.132"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-3243-7_6"},{"key":"R11","article-title":"National Center for Biotechnology Information","year":"2012"},{"key":"R12","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms5812"},{"key":"R14","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr708"},{"key":"R15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"R16","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp698"},{"key":"R17","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"R18","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv098"},{"key":"R19","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr330"},{"key":"R20","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"R21","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12549"},{"key":"R22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz305"},{"key":"R23","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg412"},{"key":"R24","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vey007"},{"key":"R25","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-016-2467-y"},{"key":"R26","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac023"},{"key":"R27","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00364-16"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001690?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T16:16:47Z","timestamp":1775837807000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001690"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,10]]},"references-count":27,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,4,10]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001690","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,10]]}}}