Anna Syme

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Note - see Jellyfish first


Genomescope takes in the histogram (the kmer profile) from jellyfish and estimates other information.

Note: Genomescope is for short reads only (e.g. Illumina), and is only for diploid genomes (although may be developed to work with polyploids also).



Or, to run on command line: genomescope.R [histogram file] [ k ] [read length] [outdir] [max kmer cov]

Results: typically, the graph shows:

The graph is also shown with logarithmic axes.

There are some statistics reported above the graph, and some in a ‘results’ box below.

My interpretation of these terms (based a lot on the supplementary paper info) is: