I've just uploaded a preprint to bioRxiv (http://www.biorxiv.org/content/early/2017/08/16/177253) that describes the Oyster River Protocol. In short, the protocol user a multi-assembler and multi-kmer approach to generating transcriptome assemblies. Because each individual assembler carries with it biases, leveraging multiple assemblers each of which complement the other results in a really great assembly. The users guide is here: http://oyster-river-protocol.readthedocs.io/en/latest/ To benchmark the protocol, I used 15 publicly available RNAseq datasets of different sizes. All were eukaryotes. Here are the highlights.
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Alejandro Sanchez-Flores
8/17/2017 09:10:38
Interesting! I must read in detail the paper and try the pipeline but as a quick question, is there any assembly correction for fused transcripts? The jaccard clip in Trinity helps but for transcriptomes from small dense genomes where UTRs overlaps it tends to fuse transcripts. Any thoughts?
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