E. coli BIGSI index

A BIGSI index of the E. coli collection which can be used to easily and quickly query the genomes for any DNA sequence of 61 bp or longer
BIGSI uses a k-mer based approach to query any DNA sequence of 61 bp or greater against all the assemblies of the collection (Bradley et al. 2019). This can be achieved as follows:

bigsi search -c config_10K_00.yaml -t 0.8
ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACA

Where config_10K_00.yaml provides the config file to the BIGSI index of the assemblies, and 0.8 is the threshold in k-mer similarity used to defined a match, and “ATGAAAAACACAATACATATCAACTTCGCTATTTTTTTAATAATTGCAAATATTATCTACA” is the sequence being search. BIGSI will return all the genome identifiers in the collection that have this sequence in at least 80% k-mer similarity. The properties of these genomes can be investigated in File F1. The user will need to ensure the path to the index is correct (“filename:”) in the config_10K_00.yaml file. Please refer to the BIGSI documentation (https://github.com/iqbal-lab-org/BIGSI) for full details.