Most big genome assemblies use pairs and mates to build their genomes.
Pairs a great but short
Mates are long and have pairs mixed-in + chimeric reads (in the sens that the
jumping juncting is IN a read)
If you have good sequencing you want want to use a big kmer to avoid repeating
regions with the pairs, but you want short kmers with the mates because of the
extra errors (with smaller kmers you could save the chimeric if your kmer ends
before the junction).
something like 61-91 for pairs
21-51 with mates.
Right now either you run everything in the middle...51-61
Use another scaffolder
Rerun your assembly in ray again with mates added (not sure if this would work)
Does this make sens or I'm missing a feature of ray that will work even with
bad reads?
Louis
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