Originally posted by beliefbio
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For clarity, if you wish to use BWA's "bwa aln" functionality for paired end reads, then you need to align each end independently, merging them together in "bfast localalign" with the "-1/-2" options. Otherwise, the paired end reads should be merged (automatically in solid2fastq) into one fastq file to be processed by "bfast match".
Originally posted by beliefbio
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Originally posted by beliefbio
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