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Forum: Bioinformatics 01-20-2015, 04:40 PM
Replies: 4
Views: 1,160
Posted By GenoMax
You can create a consensus sequence based on the...

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...
Forum: Bioinformatics 01-20-2015, 04:17 PM
Replies: 4
Views: 1,160
Posted By GenoMax
Since you have good coverage you may be able to...

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 (http://bioinf.spbau.ru/spades) is a...
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