Amplicon sequencing on MiSeq machines deliver 300 bp paired end reads and are certainly ‘better’ that 150 bp paired end reads from other machines. But ‘how much’ better are 300 bp reads? Is anybody aware of a comparative analysis of MiSeq (300 bp) and HiSeq or other (150 bp) data? From a phylogenetic perspective, longer reads (to the far end: Pacbio sequel reads) are much better to reconstruct the tree, but is this equally important for a functional perspective (the function of bacteria in a e.g. soil community, or presence of specific enzymes). I would expect that many functions/enzymes are present in a broader phylogenetic group and a high-resolution phylogenetic tree is not such important to investigate the function of microbial communities.
And it will depend on the V regions used for the analysis…
Such discussions came up when we were talking about the new Illumina iSeq-100, which can only deliver 150 bp reads.
I would very much appreciate comments from the community.