I am relativly new to bioinformatics. I have got some reads files for analysis, and these reads (fastq) actually was for a short reads sequenced sample which contain a pool of multiple bactrial species (roughly 10). all together went to the sequencer. They all belong to the same biological family, but I have the list of Genus-Specie was in that sample. But I don't know the specific strains for each.
I need to accuratly identify the strain/substr of each specie, regardless of the computation power needed to do that. example: I know that their is an e.coli in the sample but i don't know which strain? is it K12 or O157 or something else?
How can I do that? what approach to go with? and by what tools?
Thanks Best regards