comparaison to the reference genome

[mido1951]

Hello,
I generated reads a file (.fasta) I want to test the effectiveness of my file to the reference genome (before assembly).
how to do?
and what tool I have to use it to make the comparison of my file with the reference genome?
Thank you

[Brian Bushnell]

I suggest using Quast; it will compare your assembly to the reference. If you mean that you want to compare reads to an assembly, then you should use mapping, and a tool like ALE.

[mido1951]

I suggest using Quast; it will compare your assembly to the reference. If you mean that you want to compare reads to an assembly, then you should use mapping, and a tool like ALE.

to compare read file to the reference genome i should use mapping tools?
like ALE?
thanks

[Brian Bushnell]

If you want to compare reads, then map them, and then use ALE.

[mido1951]

hello,
i used BBMAP for mapping and this is the results:

   ------------------   Results   ------------------

Genome:                 1
Key Length:             13
Max Indel:              16000
Minimum Score Ratio:    0.56
Mapping Mode:           normal
Reads Used:             1626223 (793501894 bases)

Mapping:                21520.101 seconds.
Reads/sec:              75.57
kBases/sec:             36.87


Read 1 data:            pct reads       num reads       pct bases          num bases

mapped:                  84.1693%         1368781        84.7943%          672844516
unambiguous:             75.6937%         1230949        76.2771%          605259839
ambiguous:                8.4756%          137832         8.5173%           67584677
low-Q discards:           0.0000%               0         0.0000%                  0

perfect best site:       72.2714%         1175294        73.8835%          586267084
semiperfect site:        72.2780%         1175402        73.8902%          586320010

Match Rate:                   NA               NA        94.7978%          668713525
Error Rate:              13.8973%          193385         5.1976%           36664236
Sub Rate:                12.5303%          174364         0.2647%            1867550
Del Rate:                 6.0770%           84563         4.6165%           32565546
Ins Rate:                 5.8459%           81348         0.3163%            2231140
N Rate:                   0.0630%             877         0.0046%              32301

do i have good results or not?
and can explain these lines?
thanks

[mido1951]

any response?

[Brian Bushnell]

First off, it is very important to clearly explain what you did. Mapping reads to their assembly is different than mapping to a reference; which did you do? And if you have a reference, what are you making reads and assemblies for? Is this a different strain, different species, or what? What kind of data do you have, from which platform?

Those numbers are very useful when trying to determine which is a better assembly of two assemblies from the same reads, or which is a better set of reads when you have two libraries made from the same organism. However, it's hard to determine the absolute quality of an assembly just from the mapping results, since you don't know whether the mismatches are caused by misassemblies or low-quality data, or how much contamination there is, etc. The fact that 72.27% of the reads match the assembly perfectly is nice. But the fact that only 84.17% of the reads map to the assembly indicates that it is probably incomplete.