Add C. elegans genome?

[teresawlee]

Hello Endre,

Would it be possible for you to add the C. elegans genomes to your list? I would personally like you to add WS220/ce10, but it might also be useful to add the most recent assembly on UCSC, WBcel235/ce11.

Thank you for developing epic - I've found the documentation very easy to use thus far. Teresa

[endrebak]

Thanks for the request. I've started the pipeline for computing the effective genome sizes, will get back to you.

[endrebak]

The egs for C elegans with 36 length reads is 0.9386 and the chromsizes are

chrV    20924149
chrX    17718866
chrIV   17493793
chrII   15279345
chrI    15072423
chrIII  13783700
chrM    13794

You can use epic with these flags and the info above:

--effective-genome-fraction EFFECTIVE_GENOME_FRACTION, -egf EFFECTIVE_GENOME_FRACTION
                        Use a different effective genome fraction than the one
                        included in epic. The default value depends on the
                        genome and readlength, but is a number between 0 and
                        1.
  --chromsizes CHROMSIZES, -cs CHROMSIZES
                        Set the chromosome lengths yourself in a file with two
                        columns: chromosome names and sizes. Useful to analyze
                        custom genomes, assemblies or simulated data. Only
                        chromosomes included in the file will be analyzed.

I'll be gone for a week so I won't have time to update anytime soon I fear. Will be in two weeks time perhaps.

[teresawlee]

Thank you again for your help!