One of the steps during the preprocessing of the data from metatranscriptomic analysis is to remove any host reads (host contamination) by comparing to host database. But what if there is no host reference or the closest reference is the draft genome of the same family but different genus?
When there is no reference host in database, for metatranscriptomic analysis, you need to perform RNA-seq on healthy host of the same species, too.
Without any prior molecular data about a particular species, you should perform de novo-based transcriptome assembly of RNA-seq data.
In this case I will use Megahit, it is relatively fast de novo assembler.
Also removing host transcriptome is not necessary step, you can just skip the step and go for assembly.
Megahit was very useful for me in case of viruses.
In a case I used different species genome to remove host transcriptome and it was successful, but I don't know about different genus.
if there is no host genome I will go for these steps:
1- assembly with Megahit
2- identifying target organisms with blastn and blastx
3- mapping back rna-seq data to identified target organisms
4- reference guide assembly with Trinity assembler, it needs bam file of step 3
5- identifying target organisms with blastn and blastx
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