My metagenomic assembly has low coverage. What upstream steps can I adjust to increase coverage? At what possible cost? Low coverage of metagenomic assemblies must be a common problem, but I've been unable to find a "quick start guide" i.e. an outline of recommendations to remedy this, barring "do more sequencing".
From the top of my head, I am speculating that relaxing the quality cutoff score during the trimming step could help. It would give the assembler more data. Any thoughts on this? Here's my pipeline outline.
Trimmomatic (cutoff 30) -> HQ reads ->
megahit -> assembly ->
samtools -> bam files, from which I've determined the coverage is low