RNA seq assembly and CEGMA

Question

[Rahul]

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%)

Answer 1

[Rohit]

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 -

http://biorxiv.org/content/early/2015/12/30/035642

[Rahul]

Thanks, Rohit..... is there any cutoff % or value for singletons....

[Rohit]

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.