Entering edit mode
7.7 years ago
flavobacteria
▴
50
SeqMan NGen Assembly Report
SeqMan NGen 13.0.0 build 359
Assembly Time: 1:41:54
Assembly Totals
Contigs: 308
Contigs > 2K: 151
Contigs To Reach Genome Length 6000000: 309
Contigs removed due to small size: 99692
Assembled Sequences: 1329497
Unassembled Sequences: 559973
Sequences not assembled due to complete trimming: 2633
Sequences removed due to small contig size: 276798
All Sequences: 1889470
Contig N50: 48 Kbases
Average Coverage: 80
Average Totals
Sequences per Contig: 4316
Average Lengths
Contigs: 12634
Assembled Sequences: 235
Unassembled Sequences: 214
All Sequences: 229
Average Quality
Assembled Sequences: 33
Unassembled Sequences: 30
All Sequences: 33
Assembled Pair Statistics
Read Pairs: 944735
Assembled Pairs: 564044
Pairs Consistent Within a Contig: 553227
Pairs Inconsistent Within a Contig: 1469
Assembly Parameters
Match Size: 21
Match Spacing: 50
Minimum Match Percentage: 93
Match Score: 10
Mismatch Penalty: 20
Gap Penalty: 30
Max Gap: 6
Genome Length: 6000000
Expected Coverage: 73
-- SCRIPT --
setDefaultDirectory
defaultDirectory : "/Users/shicheng/Desktop/EA1/"
project
kind : genome_assembly
workflow
kind : de_novo
loadSeq
file : "/Users/shicheng/Desktop/EA1/A_CGATGT_L001_R1_001.fastq"
maxSeqs : 5000000
seqTech : IlluminaLongReads
isPair : paired
loadSeq
file : "/Users/shicheng/Desktop/EA1/A_CGATGT_L001_R2_001.fastq"
maxSeqs : 5000000
seqTech : IlluminaLongReads
isPair : paired
setPairSpecifier
{
forward : "(.*)/1"
reverse : "(.*)/2"
min : 0
max : 750
}
;Pair specified
setParam
GenomeLength:6000000
setParam
MaxGap:6
setParam
MatchSize:21
setParam
MatchSpacing:50
setParam
MinMatchPercent:93
assemble
trimEnds:true
vectScan:true
repeatScan:true
contamScan:true
doAssemble:true
removeSmallContigs
MinSeqs : 100
MinLength : 0
what do you want to comment on it? Thank you
Hi, I am guessing you want us to look at this output and evaluate whether it is "OK" or not. Evaluation of assemblies is complex and there are many metrics. To assess an assembly one would need more information, e.g. what is the organism, expected genome size, sequencing parameters etc., etc. You should run some tools, please google for "how to evaluate the quality of a genome assembly".
What is your question?
See also: Assessing The Quality Of De Novo Assembled Data