How to rebuild query genome after BWA alignment to reference genome?

[hellsingwyk]

Dear all,

I recently sequence whole genome of Mycobacterium tuberculosis(unknown strain) with around 10X to 25X. Is it possible to rebuild query genome(genome of my target sample) after bwa alignment with MTB reference ?

And What kind of other tools or setting I need to used?

Since there are other unknown strains which would be sequenced for phylogenetic analysis, their genome sequence is necessary to be retrieved.

Thank you very much for all your kindly attention!

[GenoMax]

Since you have good coverage you may be able to de novo assemble your strain's genome from the data you have and then compare it to known strains of TB.

SPAdes is a good choice for bacterial genome assembly assuming you have the right kind of data (illumina).

[hellsingwyk]

Thank you very much for your reply!!

However, is there any possible way to obtain target genome after alignment?

[GenoMax]

Thank you very much for your reply!!

However, is there any possible way to obtain target genome after alignment?

You can create a consensus sequence based on the alignments. It would only be valid for those regions where your strain matches the reference.

http://samtools.sourceforge.net/mpileup.shtml

If you use new samtools (v.1.x): http://www.htslib.org/doc/samtools-1.1.html

[hellsingwyk]

Dear GenoMax,

Thank you very much for your helpful reply!!!
I suppose my sequencing depth is suffice to cover whole reference genome.
And will that consensus sequence contain the snp and indel from my query genome?