GenomeScope

Upload results from running Jellyfish. Example: inputk21.hist

Instructions for running Jellyfish:

1. Download and install jellyfish from: http://www.genome.umd.edu/jellyfish.html#Release
2. Count kmers using jellyfish:

   $ jellyfish count -C -m 21 -s 1000000000 -t 10 *.fastq -o reads.jf

   Note you should adjust the memory (-s) and threads (-t) parameter according to your server. This example will use 10 threads and 1GB of RAM. The kmer length (-m) may need to be scaled if you have low coverage or a high error rate. You should always use "canonical kmers" (-C)

3. Export the kmer count histogram

   $ jellyfish histo -t 10 reads.jf > reads.histo

   Again the thread count (-t) should be scaled according to your server.

4. Upload reads.histo to GenomeScope

Note: High copy-number DNA such as chloroplasts can confuse the model. Set a max kmer coverage to avoid this. Default is -1 meaning no filter.