Hi everyone,
We are working on sequencing the genomes of a few bacteria and microalgae. We recently had a PacBio run which provided pretty bad results (only 76 MB of data - ~15x coverage of our ~4.5MB genome, average read length ~5,800 bp) which could not be assembled into anything coherent using HGAP. Canu assembler provided what looked like better results (106-110 contigs, N50 ~23kb) but these still covered less than one-half of the expected genome size (sum of contig length was ~2.3 MB, and our genome is estimated at ~4.5MB).
Given that we are having issues with getting high-quality DNA for PacBio from some of our cultures, we were thinking of making an Illumina library to use these reads for a hybrid assembly. Does anyone have any experience with using such a hybrid method with low-coverage PacBio data? Specifically, are there any recommended tools or parameters suggested for such an assembly?
One point to keep in mind is that our microalgae cultures are not axenic so we expect a (low) level of contaminating DNA.
Any recommendations will be very helpful.
Thanks
Daniel
We are working on sequencing the genomes of a few bacteria and microalgae. We recently had a PacBio run which provided pretty bad results (only 76 MB of data - ~15x coverage of our ~4.5MB genome, average read length ~5,800 bp) which could not be assembled into anything coherent using HGAP. Canu assembler provided what looked like better results (106-110 contigs, N50 ~23kb) but these still covered less than one-half of the expected genome size (sum of contig length was ~2.3 MB, and our genome is estimated at ~4.5MB).
Given that we are having issues with getting high-quality DNA for PacBio from some of our cultures, we were thinking of making an Illumina library to use these reads for a hybrid assembly. Does anyone have any experience with using such a hybrid method with low-coverage PacBio data? Specifically, are there any recommended tools or parameters suggested for such an assembly?
One point to keep in mind is that our microalgae cultures are not axenic so we expect a (low) level of contaminating DNA.
Any recommendations will be very helpful.
Thanks
Daniel
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