Suggestions for Alternate Assembly Resources to Trinity
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5 weeks ago
kacollier • 0

As far as I can tell, Galaxy no longer seems to support Trinity as an assembler - or at least, I have not been able to assemble any read data using Trinity for the past several months. Initially, I had had success in assembling datasets locally using SPAdes (via Phyluce), but for large datasets (>200MB), I run into a significant RAM limitation.

Does anyone else know of a good service to run an assembler (preferably, but not essentially, Trinity) non-locally? Neither the Cipres Portal or CyVerse appear to host either it (or SPAdes), and I was wondering what other solutions people have come up with. Our lab handles primarily avian UCE data, in the form of Illumina paired-end reads.

assembly trinity HPC • 81 views
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