How To Calculate Genome Size From Scaffolds?

Question

[Naren]

1. I have a assembly fasta file for all scaffolds of a microbe.
   Can direct count of bases in the file be taken as its GENOME SIZE.

2. I also have Genebank scaffold file another way I added counts of each scaffold length in bp.

Which is more correct GENOME SIZE of that microbe?

Answer 1

[Adrian Pelin]

You can only calculate assembly size and not genome size. If all scaffolds are your microbe with no contamination, and if these scaffolds are not missing any part of the genome, then assembly size is genome size. Same applies to genbank file, it is no different.

Check this script to calculate assembly size from fasta file: http://korflab.ucdavis.edu/datasets/Assemblathon/Assemblathon2/Basic_metrics/assemblathon_stats.pl