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Old 02-10-2012, 08:58 AM   #1
Location: Guelph, Ontario, Canada

Join Date: Jan 2012
Posts: 31
Default De novo transcriptome quality metrics?

Hi everyone

I'm going to be making several de novo transcriptome assemblies (using different software), and I wish to compare them. What metrics are best for this? I don't have a reference genome.

Also, is there a software package for generating these metrics from output files? I've currently tried running Trinity, and I get a lot of output files, but none that seem to summarize the number of contigs, their length, etc. How can I calculate this from a fasta file of assembled contigs?
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