Hello, I am new to bioinformatics analysis, and I am currently running a set of complex soil samples via qiime2-moshpit-2025.7 installed via conda. I am posting to hopefully resolve an issue with my assembly generating a low percentage of map reads to scaffold (34%) and a low-quality binning (2.44%). I will link a table that outlines my diagnostic percentages. I am currently using the default megahit and metaBAT parameters (as seen on the moshpit tutorial pdf) for assembly and binning. I am wondering whether co-assembly and binning of replicates would increase this, or whether I should adjust my assembly and binning parameters. Ex. using meta-large or meta-sensitive
My workflow is as current workflow is as follows:
- demux
- cutadapt-trimmed paired
- megahit assembly
- index contigs
- map reads to contigs
- bin contigs with metaBAT
- bin evaluation with BUSCO
I have more downstream analysis planned, but testing to get an optimized assembly prior.
Any advice or assistance would be greatly appreciated. My apologies if I have misused the forum in any way. I cannot currently identify any troubleshooting tips for this situation.