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

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Posts: 41
Exclamation Soap De Novo assembly interpretation

Hello!

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:
.arc
.contig
.contigIndex
.edge
.updated.edge
.gapSeq
.kmerFreq
.links
.markonEdge
.newContigIndex
.path
.peGrads
.preArc
.preGraphBasic
.readInGap
.readOnContig
.scaf
.scaf_gap
.scafSeq
.vertex

Thanks so much for the help!!
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Old 08-12-2013, 01:35 PM   #2
vivek_
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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
jebowers
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A file called .scafStatistics should have the basic information on N50, total size of assembly etc.
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assembly quality, contig size, soap denovo

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