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In recent years, infections with <jats:italic>E. coli<\/jats:italic> have increased worldwide and so has the emergence of antibiotic resistant strains. In the present study we have assembled, annotated and analysed genome sequences of three strains of the phylogroup D of <jats:italic>E. coli<\/jats:italic>. These strains were isolated from the river Yamuna, a prominent anthropogenic urban river of northern India. These strains showed varied antibiotic susceptibilities, one was susceptible to all the antibiotics tested except ampicillin while of the other two, one was multi-\u03b2-lactam resistant and the other was multi-drug resistant (resistant to multiple \u03b2-lactams, fluoroquinolones and kanamycin). The short-sequence reads were assembled into contigs using the <jats:italic>de-novo<\/jats:italic> approach and further, scaffolding of contigs was performed by using the best reference genome for a particular isolate which resulted in a significant increase in the N<jats:sub>50<\/jats:sub> value of each assembly. The bioinformatics assembly approach used in this study could be easily applied to study other bacterial genomes.<\/jats:p>","DOI":"10.1038\/s41597-023-02444-0","type":"journal-article","created":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T13:02:42Z","timestamp":1693573362000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Genomic analysis of phylogroup D Escherichia coli strains using novel de-novo reference-based guided assembly"],"prefix":"10.1038","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9088-7017","authenticated-orcid":false,"given":"Manisha","family":"Aswal","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0851-6434","authenticated-orcid":false,"given":"Neelja","family":"Singhal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7936-9892","authenticated-orcid":false,"given":"Manish","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2023,9,1]]},"reference":[{"key":"2444_CR1","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1111\/j.1365-2958.2006.05172.x","volume":"60","author":"T Wirth","year":"2006","unstructured":"Wirth, T. et al. 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