IMG MER Metadata availability questions

[bjkr...@umn.edu]

Is information available for omics projects in regards to the average coverage per scaffold or contig from an assembly? Also, I know that the metadata is available on IMG/MER for the estimated genome size of a project, but is there any information/metadata option for how estimated genome sizes are determined?

[Rekha Seshadri]

There is *some info* in the IMG glossary doc: https://img.jgi.doe.gov/docs/IMG_GOLDTerms.pdf

E.g., Scaffold Read Depth (also referred to as scaffold/contig average coverage) is the average number of reads aligned to each base of the contig. Read depth is calculated by aligning the reads to the contig and can be extracted from the output of read aligner, such as bbmap or Bowtie.

Estimated genome size for a metagenome sample is quite simply the total assembled metagenome size (ib bp) divided by the estimated number of genomes. The latter is a measure of species "richness" derived by computing the mean, median, mode of universally conserved single copy marker genes ad the median value is reported as the est. number of genomes so long as the std dev is reasonable.

Est. genome size is a very rough measure for exploratory purposes IMO. Proceed with caution. :)

Hope that clears it up!