Question: How to calculate effective genome size using unique-kmers.py from khmer program?
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gravatar for salamandra
4 months ago by
salamandra180
salamandra180 wrote:

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?

ADD COMMENTlink modified 4 months ago • written 4 months ago by salamandra180

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/#

ADD REPLYlink written 4 months ago by h.mon22k
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