Published June 21, 2023 | Version v1
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Searching for shared sequence between Mycobacterium tuberculosis and Homo sapiens

  • 1. Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne

Description

In this short report, I explore whether Mycobacterium tuberculosis and Homo sapiens share genomic sequence through shared k-mer analysis and simulated read alignment. You can read the HTML version on my website.

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References

  • Nilgiriwala K, Rabodoarivelo M-S, Hall MB, Patel G, Mandal A, Mishra S, et al. Genomic sequencing from sputum for tuberculosis disease diagnosis, lineage determination, and drug susceptibility prediction. J Clin Microbiol. 2023;61: e0157822. doi:10.1128/jcm.01578-22
  • Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, et al. The complete sequence of a human Y chromosome. bioRxiv. 2022. doi:10.1101/2022.12.01.518724
  • Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393: 537–544. doi:10.1038/31159
  • Wick R. Badread: simulation of error-prone long reads. J Open Source Softw. 2019;4: 1316. doi:10.21105/joss.01316
  • Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34: 3094–3100. doi:10.1093/bioinformatics/bty191
  • Jain C, Rhie A, Hansen NF, Koren S, Phillippy AM. Long-read mapping to repetitive reference sequences using Winnowmap2. Nat Methods. 2022;19: 705–710. doi:10.1038/s41592-022-01457-8
  • Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012;28: 593–594. doi:10.1093/bioinformatics/btr708