I've got a question regarding the assembly of PacBio reads. We've created a library of approximately 5000 different amplicons between 1 and 3kb and successfully ran these on a couple of flow cells. Next we've ran the RS_ReadsOfInsert protocol and demultiplexed the data with the corresponding barcodes.
The next step is to align/assemble these reads to each other to build contigs of multiple reads mapping to the same consensus. However the majority of the tools (HGAP, Quiver) that I come across are designed to do (de novo) genome assembly, that is not what we are aiming at, we "just" want to align/assemble the PacBio demultiplexed reads and build contigs from 1-3 kb.
What tool would be the best to perform this job?
The next step is to align/assemble these reads to each other to build contigs of multiple reads mapping to the same consensus. However the majority of the tools (HGAP, Quiver) that I come across are designed to do (de novo) genome assembly, that is not what we are aiming at, we "just" want to align/assemble the PacBio demultiplexed reads and build contigs from 1-3 kb.
What tool would be the best to perform this job?
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