How can I effectively perform metagenomic assembly on large Illumina sequencing data from environmental samples, given that I have already completed quality control but encounter issues due to the data size?
Several online resources you might try have limitations, so whether they work or not will depend on how much data you have. Most of them perform other analyses besides assembly, so you might consider what to do with the results and check if other tools available on the same site could also help.
You could try:
EDGE https://nmdc-edge.org/home
Mgnify https://www.ebi.ac.uk/metagenomics
KBase https://www.kbase.us/
Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/
I agree with the previous answer. However, generating the assemblies is sometimes helpful, so what I would do is: remove low-quality and short reads (as much as possible; you can be stringent if the coverage is high) and second, subsampling (random subsampling, i.e., 50%, 25%, etc.).