please help look at the output for my assembly of bacterial genome using DNASTAR
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6.0 years ago
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
Assembly Forum • 1.7k views
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what do you want to comment on it? Thank you

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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".

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What is your question?

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