Question: merge aligned read pairs that overlap - keep the bases that match the reference
gravatar for Richard
2.3 years ago by
Richard570 wrote:

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

paired-end illumina • 668 views
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