Genome assemblies

All reads (both short- and long-read) have been submitted to NCBI under the project ID PRJNA1254181 (but are not yet publicably available).

The genomes were mainly assembled using hybracter which assembles long-reads and polishes with short-reads (i.e. a long-read first hybrid assembly) to produce accurate and complete genomes. Some were also assembled using flye (long-read only) and unicycler (short-read first hybrid assembly)

For more information about how the genomes were assemblied see the methods section of the associated preprint on BioRxiv:

Goodman, R.N., Moyo, S.J., Memelis, I., Khanijau, A., Manyahi, J., Kibwana, U.O., Aboud, S., Blomberg, B., Langeland, N. & Roberts, A.P. (2025) Genomic comparison of highly related pairs of E. coli and K. pneumoniae isolated from faeces and blood of the same neonatal patients hospitalized with fever in Dar es Salaam, Tanzania. bioRxiv. doi:10.1101/2025.04.28.650962.