{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T00:09:23Z","timestamp":1747181363923,"version":"3.40.5"},"reference-count":14,"publisher":"Microbiology Society","issue":"6","license":[{"start":{"date-parts":[[2022,6,30]],"date-time":"2022-06-30T00:00:00Z","timestamp":1656547200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,30]]},"abstract":"There is a need to identify microbial sequences that may form part of transmission chains, or that may represent importations across national boundaries, amidst large numbers of SARS-CoV-2 and other bacterial or viral sequences. Reference-based compression is a sequence analysis technique that allows both a compact storage of sequence data and comparisons between sequences. Published implementations of the approach are being challenged by the large sample collections now being generated. Our aim was to develop a fast software detecting highly similar sequences in large collections of microbial genomes, including millions of SARS-CoV-2 genomes. To do so, we developed Catwalk, a tool that bypasses bottlenecks in the generation, comparison and in-memory storage of microbial genomes generated by reference mapping. It is a compiled solution, coded in Nim to increase performance. It can be accessed via command line, rest api<\/jats:sc> or web server interfaces. We tested Catwalk using both SARS-CoV-2 and \n \n Mycobacterium tuberculosis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> genomes generated by prospective public-health sequencing programmes. Pairwise sequence comparisons, using clinically relevant similarity cut-offs, took about 0.39 and 0.66 \u03bcs, respectively; in 1 s, between 1 and 2\u2009million sequences can be searched. Catwalk operates about 1700 times faster than, and uses about 8\u200a% of the RAM of, a Python reference-based compression and comparison tool in current use for outbreak detection. Catwalk can rapidly identify close relatives of a SARS-CoV-2 or \n \n M. tuberculosis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> genome amidst millions of samples.<\/jats:p>","DOI":"10.1099\/mgen.0.000850","type":"journal-article","created":{"date-parts":[[2022,6,30]],"date-time":"2022-06-30T15:16:20Z","timestamp":1656602180000},"source":"Crossref","is-referenced-by-count":0,"title":["Catwalk: identifying closely related sequences in large microbial sequence databases"],"prefix":"10.1099","volume":"8","author":[{"given":"Denis","family":"Volk","sequence":"first","affiliation":[{"name":"Nuffield Department of Medicine, University of Oxford, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fan","family":"Yang-Turner","sequence":"additional","affiliation":[{"name":"Present address: UKRI Science and Technologies Facilities Council, Harwell, UK"},{"name":"Nuffield Department of Medicine, University of Oxford, Oxford, 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":"Department of Statistics, University of Warwick, Coventry CV4 7AL, UK"},{"name":"School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Derrick W.","family":"Crook","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, University of Oxford, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9155-6228","authenticated-orcid":false,"given":"David","family":"Wyllie","sequence":"additional","affiliation":[{"name":"UK Health Security Agency, Forvie Site, Addenbrookes\u2019 Campus, Robinson Way, Cambridge CB2 0SR, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-00838-z"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1016\/j.lana.2021.100018"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1800474"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2019.03.022"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1008357"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2104241118"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-021-00573-0"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-017-1907-2"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-538"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2018.07.030"},{"year":"2021","key":"R11","article-title":"Cython documentation and source code: setobject.c"},{"year":"2021","key":"R12","article-title":"C++ symmetric difference set algorithm"},{"key":"R13","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2021.07.034"},{"year":"2021","key":"R14","article-title":"FindNeighbour4: a server application for investigating bacterial relatedness using reference-mapped data"}],"container-title":["Microbial Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000850?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T20:27:47Z","timestamp":1702585667000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000850"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,30]]},"references-count":14,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2022,6,30]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.000850","relation":{},"ISSN":["2057-5858"],"issn-type":[{"type":"electronic","value":"2057-5858"}],"subject":[],"published":{"date-parts":[[2022,6,30]]}}}