[maker-devel] Transcriptome Assmeblies for Protein Evidence

[Li, Michael]

Hi everyone,

I've been tasked to run MAKER on a genome that we have recently sequenced and assembled de novo. Along with the genome, the transcriptome has also been assembled using SOAPdenovo. I've been told that we've experimented with different kmers, but I'm not sure which kmer is ideal for use.

One kmer assembly has the highest N50 for contigs, while another has the highest N50 for scaffolds, but it comes with a lot of gaps.

Would gaps impact how MAKER handles evidence alignment or the overall annotation? Or would either work well with MAKER?

Thanks in advance!

Michael Li
Co-op Student