How to calculate effective genome size using unique-kmers.py from khmer program?
Here says that to know effective/mappable genome size with multimapping reads excluded we need to use 'unique-kmers.py' from 'khmer'. I installed the program, but do not understand the help page and do not know how to use the options. Does anyone know of an example of it's use for calculating effective genome size?
According to help page it is counting kmers. Is counting kmers the same as estimating effective genome size?
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Do you need to use khmer? There are a number of other options, with detailed instructions / tutorials:
http://seqanswers.com/forums/showthread.php?t=48375
Genome size estimation discrepancy : Jellyfish k-mer Vs. estimate_genome_size.pl
https://bioinformatics.uconn.edu/genome-size-estimation-tutorial/#