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Old 06-04-2015, 08:03 AM   #7
Location: Germany/Netherlands

Join Date: Feb 2014
Posts: 98

There are tools like CGAL and RSEM-EVAL, which calculate the likelyhood of the reads belonging to the actual assembly. That might help when you're having more than 1.

Since sometimes the size of the assembly can vary too, I also like to have an estimate of the genome size beforehand, tools to use are kmerspectrumanalyzer or kmergenie.

And depending on how fragmented you can/want to get with the data: A most likely correct genome (not necessarily contigous) will be to take the consensus from all your assemblies, and break the contigs if they're not agreeing.

<s>If you arrive at a chromosome, and you have a prokaryote, then you need to take a look at the GC skew of the chromosome to detect obvious misassemblies.</s> scratch that, didn't see the transcriptome part.
EDIT: Eh, no strike through tags in this forum?
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