Hi, everyone, I have two metagenomic samples, I co-assembled these samples together using both spades and Megahit and then I mapped each sample against the co-assembly using bowtie2. I got for each sample around 40 % overall alignment rate. I would like to know if this low value is normal (given that the assembly comes from reads of both samples)???
Its not necessarily low...
If it's host metagenomes you might have the host reads. Try mapping to the host genome.
If it doesn't help much would try assembly separately to each sample.
Remember that the assembly quality is affected by the read length, sequencing depth and the diversity of the samples.
Good luck :)