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Tool for de novo assembly evaluation ??

Hello,

I've ran Soapdenovo, which produce a statistic file (scafStatistics).

However the N50 is different from the one produced by QUAST ...

Do you have an idea what is wrong ?

By the way, do you know a fast tool for computing assembler statistics such as N50, contig number etc.

soap quast
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written by Picasa Picasa

2 answers

We've used the assemblathon script for this for quite a while, but there are likely better ones out there now.

http://korflab.ucdavis.edu/datasets/Assemblathon/Assemblathon2/Basic_metrics/assemblathon_stats.pl

Re: variation in N50, it may be dependent on whether the tool is reporting the stats on raw vs. a filtered (removing seqs less than a minimum cutoff). We generally perform both, and if at all possible use an estimated genome size so the metrics (NG50 in this case) can be compared more readily across assemblies.

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written by Chris Fields Chris Fields

Is assemblathon script permors filtering before computing N50 ?

Cause I have different result compare to Soapdenovo and QUAST.

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written by Picasa Picasa

For future reference, you should add this as a reply to my answer, not add this as another answer.

The script processes the sequences as is and performs no filtering; the other tools may give different results depending on whether they pre-filter or not. TBH I'm not sure.

EDIT: Also, make sure the N50 you're comparing is contig or scaffold-based (and whether there are any minimal N counts needed to split scaffolds into contigs).

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written by Chris Fields Chris Fields

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