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!!
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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