Hi all,
I am currently trying to assemble a ~400 Mb plant genome using Newbler version 2.8. I have Illumina Hi-Seq paired-end reads (135 M reads), 90 bp with 500 bp insert. Below is the statistics:
//scaffoldMetrics
avgScaffoldSize = 50577;
N50ScaffoldSize = 162943, 320;
largestScaffoldSize = 3497334;
avgScaffoldContigSize = 4054;
N50ScaffoldContigSize = 7987, 7459;
largestScaffoldContigSize = 212004;
scaffoldEndMetrics
NoEdges = 9582, 91.2%;
OneEdge = 0, 0.0%;
TwoEdges = 0, 0.0%;
ManyEdges = 0, 0.0%;
LargeRep = 920, 8.8%;
scaffoldGapMetrics
BothNoEdges = 45419, 88.8%;
OneNoEdges = 5347, 10.5%;
BothOneEdge = 0, 0.0%;
MultiEdges = 0, 0.0%;
LargeRep = 356, 0.7%;
largeContigMetrics
numberOfContigs = 68739;
numberOfBases = 238994887;
avgContigSize = 3476;
N50ContigSize = 7521;
largestContigSize = 212004;
Q40PlusBases = 237415811, 99.34%;
Q39MinusBases = 1579076, 0.66%;
largeContigEndMetrics
NoEdges = 129091, 93.9%;
OneEdge = 0, 0.0%;
TwoEdges = 0, 0.0%;
ManyEdges = 0, 0.0%;
LargeRep = 8387, 6.1%;
//
Google tells me that "NoEdges" means the assembly is bad.
Any advices?
Thank you!
I am currently trying to assemble a ~400 Mb plant genome using Newbler version 2.8. I have Illumina Hi-Seq paired-end reads (135 M reads), 90 bp with 500 bp insert. Below is the statistics:
//scaffoldMetrics
avgScaffoldSize = 50577;
N50ScaffoldSize = 162943, 320;
largestScaffoldSize = 3497334;
avgScaffoldContigSize = 4054;
N50ScaffoldContigSize = 7987, 7459;
largestScaffoldContigSize = 212004;
scaffoldEndMetrics
NoEdges = 9582, 91.2%;
OneEdge = 0, 0.0%;
TwoEdges = 0, 0.0%;
ManyEdges = 0, 0.0%;
LargeRep = 920, 8.8%;
scaffoldGapMetrics
BothNoEdges = 45419, 88.8%;
OneNoEdges = 5347, 10.5%;
BothOneEdge = 0, 0.0%;
MultiEdges = 0, 0.0%;
LargeRep = 356, 0.7%;
largeContigMetrics
numberOfContigs = 68739;
numberOfBases = 238994887;
avgContigSize = 3476;
N50ContigSize = 7521;
largestContigSize = 212004;
Q40PlusBases = 237415811, 99.34%;
Q39MinusBases = 1579076, 0.66%;
largeContigEndMetrics
NoEdges = 129091, 93.9%;
OneEdge = 0, 0.0%;
TwoEdges = 0, 0.0%;
ManyEdges = 0, 0.0%;
LargeRep = 8387, 6.1%;
//
Google tells me that "NoEdges" means the assembly is bad.
Any advices?
Thank you!
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