merge aligned read pairs that overlap - keep the bases that match the reference
Hi all,
I have aligned paired-end genome data that was sequenced with 150bp reads. The average insert size is just 200bp so there are lots of read pairs with significant overlap of their alignments.
I see that there are lots of tools for merging fastq data and at least one that clips overlapping read alignments.
I'm looking for a tool that uses a conservative approach that when merging or clipping overlapped read alignments, chooses the bases that match the reference over bases with high sequencing quality.
thanks, RIchard
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