Merge / Reconciliate several de novo transcriptome assemblies with different kmers I am building a De Novo transcriptome reference assembly for an eukaryotic organism for which I have a genome.
I've created several assemblies with rnaSpades using different kmer sizes (19 to 69 with step 10). Now I would like to merge them into one final transcriptome.
How could I do that?
Is using a genome assembly reconciliation tool such as metassembler a good idea?
You may combine all your transcriptomes into a single file and then apply a clustering method to group very similar transcripts into a single one. For that purpose, you may try CD-HIT-EST or MMseqs2. For each identity threshold you are going to test, you may assess the final quality with BUSCO or by blasting against reference sequences.