Merge / Reconciliate several de novo transcriptome assemblies with different kmers

A simple option would be to simply supply SPAdes with some contigs that you like with the --trusted-contigs option.

There exist tools specifically addressing the problem of merging transcriptome assemblies. I am unsure whether this is notably different from genome assemblies sufficiently that they are better than the genome assembly mergers. Here is a partial list:

1. transfuse
2. this paper
3. this paper
4. this paper
5. DRAP

This paper seems to have some more information on comparing tools, though it is not focused specifically on merging.

See also the SeqAnswers on this topic, and this discussion too.

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.