This would be for assemblies with large scaffolds and small contig sizes. For example, a 10X genomics only denovo assembly or an Illumina + HiC (dovetail) assembly. One would think adding PacBio data, even at low coverage, would increase the contig sizes by a lot. So far the papers I have seen only show modest gains with PB Jelly and PacBio data.
We used it with PacBio, Illumina and Nanopore data and it worked
Good to know! What were your N50 contig and N50 scaffold sizes before and after running PBJelly. Did PacBio and Nanopore work equally well or did you just combine the long read data before running PBJelly?
You can see assembly statistics from the supplementary material of our paper using PBJelly to fill in gaps in a Illumina assembly scaffolded with Dovetail Chicago and Dovetail Hi-C data.
Article Improving Illumina assemblies with Hi-C and long reads: An e...
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