Bin-assembled Escherichia coli genomes from a study in Punjab, Pakistan

Bin-assembled Escherichia coli genomes from Punjab, Pakistan

These assemblies are a part of a cross-sectional study conducted in Punjab, Pakistan aimed at investigating E. coli colonisation diversity in healthy carriage with the use of CLED enrichment plates.

About

Version history

v0.1.1 (current version)

• Added reference to the study.

v0.1.0

• Added brief description with a few missing parts.

Distribution

If you use these assemblies in your study please cite the source as appropriate. These assemblies are made available under a CC-BY 4.0 license.

Citation

Khawaja, T., Mäklin, T., Kallonen, T. et al. Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan. Nature Communications 15, 5196 (2024). https://doi.org/10.1038/s41467-024-49591-5

Methods briefly

Species identification

Sequencing data from the ENA project PRJEB36642 was error-corrected with fastp and pseudoaligned with Themisto against a species-level index (available from https://doi.org/10.5281/zenodo.6656881). Reads were assigned to species using the mSWEEP/mGEMS pipeline as described in https://www.nature.com/articles/s41467-022-35178-5.

Lineage identification

Read from the species-level bins were again pseudoaligned with Themisto against an E. coli index (will be made available in a later version). Lineage-level assignment was performed using mSWEEP and mGEMS at the level of PopPUNK sequence clusters. The created bins were screened with demix_check and bins that received a score of 1 or 2 were kept. Data in the kept bins were assembled with shovill and the bin-assembled genomes (BAGs) were quality controlled with checkm for >= 90% completeness and <= 10% contamination. Finally, BAGs shorter than 4 Mb or longer than 6 Mb were removed.

Contact

Tommi Mäklin <tommi'at'maklin.fi>.