Estimated genome size using mash sketch

[MostafaYA]

Hello,

I understand that mash sketch can gives rough estimation about the genome size based on the unique kmers in the sample.

I using the following command for this purpose, to roughly estimate genome size of bacteria
mash sketch -o tempFile -k 32 -m 3 -r read1.fastq
In most cases, I am getting estimations of bacterial genomes close to real size (size mentioned in literatures)
In some cases, however, there is a great discrepancy between the estinated genome and the real size.
Does that mean

• the original sample may not be fully sequenced in case that the estimated value of the genome size is far too low than normal?
• the original sample may be contaminated in case that the estimated value of the genome size is far too high than normal?

I would appreciate if you declare any misunderstanding from my side

[ondovb]

Those both sound like reasonable explanations. A good check might be to run mash screen on your reads against RefSeq (see https://mash.readthedocs.io/en/latest/tutorials.html#screening-a-read-set-for-containment-of-refseq-genomes). This will tell you, roughly, how well your genome is covered (or at least its nearest RefSeq neighbor) and if there are significant contaminants.

[tseemann]

@MostafaYA are these Illumina reads?

[MostafaYA]

@tseemann Yes, they are MiSeq Illumina reads

[tseemann]

To estimate genome size in shovill I do the same as what you have done -k 32 -r -m 3. If you have very high coverage you could try increasing to -m 10, or if you have high error rate try reducing to -k 24. Also, only use R1 as it is higher quality, esp on MiSeq.

Secondly, just do a genome assembly of the reads with Shovill, SKESA or Spades. If the total contig size is too high, you probably have contamination, or not a pure colony.

[MostafaYA]

@tseemann @ondovb Thanks a lot your answers