It definitely is advisable, but not sure if possible. At least the earlier versions of trinity (2-3 years ago) had fixed kmer sizes in chrysalis step (clustering), but other steps can use a user-defined kmer. Additionally, there was an upper bound of 32 for kmer length.
k-mer optimization in Trinity
Hi all,
As far as I know the k-mer in the trinity software is almost constant (25), I would like to know if it should be changed and optimized to make the best transcriptome assembly from about 400 million reads. any suggestion would be highly appreciated.
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