How to identify different bacterial strains in the same sample

[shiningway]

I have Illumina sequencing of a bacterial sample collected from a patient. I suspect it's a mixture of multiple strains of the same bacteria, but I don't which strains are in there. Is there anyway to identify

1. if this sequence sample is a mixture of different strains?

2. how many and what strain are in there?

Thanks.

[GenoMax]

How to do this in practice: http://seqanswers.com/forums/showthread.php?t=16812

Analysis (see post #2) in this thread: http://seqanswers.com/forums/showthread.php?t=31565

[shiningway]

Thanks. I'm not sure how this would help in my case. I'm not trying to do any phylogeny analysis. I just need to know if sequence I have was from one pure bacterial strain or from multiple strains.

How to do this in practice: http://seqanswers.com/forums/showthread.php?t=16812

Analysis (see post #2) in this thread: http://seqanswers.com/forums/showthread.php?t=31565

[GenoMax]

Thanks. I'm not sure how this would help in my case. I'm not trying to do any phylogeny analysis. I just need to know if sequence I have was from one pure bacterial strain or from multiple strains.

My fault. The title on your original post made it sound (to me) like you were interested in identifying bacterial strains not specifically strains of the same species.

If the strains are expected to have small differences then this would be a difficult problem.