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Old 04-08-2015, 02:37 AM   #2
Michael.Ante
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Location: Vienna

Join Date: Oct 2011
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You can download the virus sequences in fasta format and use e.g. Bowtie2 to align the reads locally. Therefore, you need to build an index first. The log output of Bowtie2 tells you haw many reads mapped.
After aligning the reads, you can use samtools to get some statistics (e.g. samtools idxstats).
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