Hello I'm from Mexico

[ppbto]

I'm a masters student of biochemical sciences.

I have some questions: is posible know the genome size by NGS? and if it's posible how much do you need to sequence to have a good estimate?

[lcollado]

Hello ppbto,

You should ask your question in the bioinformatics forum instead of the Introductions one. Anyhow, as I understand it your question is:

Is it possible to estimate the genome size only by using HTS data? If it is possible, what sequencing depth do you need to obtain an accurate estimate? 2x? 4x?

Greetings,
Leo

[lcollado]

Hello again,

Check the paper on the Panda genome http://dx.doi.org/10.1038/nature08696 . It doesn't answer your question completely, but it's a start.

To assess genome coverage of the assembled contigs and scaffolds,
we first estimated the genome size of the panda. To obtain the best
estimate, we used sequencing depth, size ratio of syntenic blocks, and
comparison of C-values. Using 17-base oligonucleotides and their
frequency distribution in the usable sequencing reads to determine
sequencing depth11, we obtained an estimated panda genome size of
2.46 Gb (Supplementary Fig. 8). Given the presence of sequencing
errors, we expect that the sequencing depth is underestimated, and
consequently the panda genome size should be slightly smaller than
2.46 Gb.

Greetings,
Leo