Hello,
Here is my assembly report. I am not sure whether my assembly statistic results are acceptable or not.I would be very grateful for any comment on the following report.
<-- Information for assembly Scaffold 'SoapTransOut.scafSeq'.(cut_off_length < 100bp) -->
Size_includeN 47160083
Size_withoutN 46439055
Scaffold_Num 109706
Mean_Size 429
Median_Size 143
Longest_Seq 11475
Shortest_Seq 100
Singleton_Num 84198
Average_length_of_break(N)_in_scaffold 6
Total_scaffold_length_as_percentage_of_known_genome_size NaN
scaffolds>100 107601 98.08%
scaffolds>500 25379 23.13%
scaffolds>1K 13734 12.52%
scaffolds>10K 2 0.00%
scaffolds>100K 0 0.00%
scaffolds>1M 0 0.00%
N10 2755 1341
N20 2073 3340
N30 1661 5890
N40 1336 9057
N50 1046 13033
N60 756 18323
N70 481 26114
N80 272 39414
N90 124 67131
Number_of_contigs_in_scaffolds(Singleton) 84198
Number_of_contigs_not_in_scaffolds 64167
Average_number_of_contigs_per_scaffold 1.4
CEGMA completeness report:- (Complete) 85%, Partial (96%)
1 answer
No idea what acceptable is since your species is unknown.. if non-model organism then it would be difficult to say. Try out BUSCO validation tool, CEGMA is a great start but support is discontinued and they too suggest busco. For a better picture, read -
If by singletons you mean the contigs which are present in scaffolds, the more the better - so no golden % if that's what you are looking for. But this is highly influenced by the complexity of the genome (repeats,coverage etc). If you have multiple libraries, this would not be a problem as repetitive regions can be scanned by mate-pair libraries or long-read technologies.
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