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Old 05-12-2015, 07:24 PM   #5
Brian Bushnell
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Location: Walnut Creek, CA

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Old thread, but BBMap has a stats.sh program that will summarize basic assembly stats (N50, L50, distribution of contig sizes, GC%, etc); it's very fast even on assemblies with millions of contigs, and extremely easy to use:

stats.sh contigs.fasta

For more advanced statistics, particularly if you have a reference and are evaluating different assembly methodologies, I recommend Quast because it also does alignment to the reference to calculate the number of misassemblies. Also, even if you don't have a reference, it does neat things like gene prediction. Not sure how that feature would work on a transcriptome, though.

Last edited by Brian Bushnell; 05-12-2015 at 07:26 PM.
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