Effective Genome Size — deepTools 3.5.6 documentation (original) (raw)

A number of tools can accept an “effective genome size”. This is defined as the length of the “mappable” genome. There are two common alternative ways to calculate this:

1. The number of non-N bases in the genome.
2. The number of regions (of some size) in the genome that are uniquely mappable (possibly given some maximal edit distance).

Option 1 can be computed using faCount from Kents tools. The effective genome size for a number of genomes using this method is given below:

These values only appropriate if multimapping reads are included. If they are excluded (or there’s any MAPQ filter applied), then values derived from option 2 are more appropriate. These are then based on the read length. We can approximate these values for various read lengths using the khmer program program and unique-kmers.py in particular. A table of effective genome sizes given a read length using this method is provided below: