Question on conducting waafle_junctions.py by single-end read

Microbial community profiling WAAFLE
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Hi there! I have a question for what if using single-end read when conducting waafle_junctions step. Since the program need paired-ends reads or SAM file. Thank you in advance~

Xinming

1 Like
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Same question here, would be helpful with long read sequencing data.

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Sorry to have missed the original question here. We don’t currently have a way to run the QC pipeline in WAAFLE within single-end reads. The pipeline was developed with the assumption that end-pairing would be informative for QC, although it would be possible to adapt the pipeline to work without this information. I’ll make a note about this for the future.

If you’re providing long reads as input to WAAFLE (in lieu of contigs) then you wouldn’t even need to perform this step, as its primary purpose is to weed out misassembly events.

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Great :slight_smile: thanks very much for all the wonderful tools you guys create and maintain!