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Old 08-12-2013, 12:59 PM   #1
Location: USA

Join Date: Sep 2012
Posts: 41
Exclamation Soap De Novo assembly interpretation


I have run soap de novo on my assembly, and I have used different kmers. I have 12 assemblies and I need to choose the best one out of those 12.
There are around 21 files created in each of the 12 assemblies.
My question is, how should I interpret these files so as to choose the best assembly (things like n50, contig size-max,min; no. of contigs, coverage, assembly size etc).
Which files should I use to get these results?
The 21 files are:

Thanks so much for the help!!
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Old 08-12-2013, 01:35 PM   #2
PhD Student
Location: Denmark

Join Date: Jul 2012
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I worked on SOAP assemblies a while ago and I think .scafseq is the fasta file of the scaffolded sequences and you'd likely be evaluating the contiguity metrics of your assemblies on this one. I can't remember the name for the contig fasta file.
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Old 08-13-2013, 08:38 AM   #3
Location: Athens, GA, USA

Join Date: Apr 2013
Posts: 19

A file called .scafStatistics should have the basic information on N50, total size of assembly etc.
jebowers is offline   Reply With Quote

assembly quality, contig size, soap denovo

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