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Old 07-14-2014, 05:27 AM   #4
sdmoore
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Location: Florida

Join Date: Jun 2014
Posts: 11
Default the PRICE was right

I wanted to update the thread to say that PRICE did the trick.

At first, I had trouble getting contains to extend into certain regions (which were ambiguous in the maps as well). After consulting with the author (who was more than helpful), I ended up combining my reads into a single file and using the input option "-spfp [file.fastq]", which basically cuts each read in half and uses them as their own read pairs during assembly. This strategy avoids stalling caused by read pairs that contain substantial overlap with the partner (these were 300 base reads from a ~400 fragment library before processing, so there was likely to be a lot of overlap).

Once optimized (adjusting kmer, cut size, percent match, etc.), I could feed in a ~300 nt sequence from a region and let it grow over a region of interest. It resolved several ambiguous sites and also identified an IS insertion in one of the genes of interest (which was missed by BWA-mem, but "noisy" in Bowtie2).

I also easily assembled a plasmid that was in one of the strains using seed "contigs" from known regions. We had never fully sequenced it and this was bonus data.

Thanks again for the pointer.
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