Hello
When I finished binning with MetaBAT, I found there is no bins in the output. Then, I check the commands, I found Minimum size of a contig should be >=1500 for binning. But the N50 of the assembed contigs from Illumina platform is only 500bp. In this case, should I combine all the sample data? Or the MetaBAT is not suitable for Illumina data?
The problem is that your assembly has extremely short contigs. 500bp is the length of the reads for in some configurations of Illumina data. 1500 base contigs in the assembly is the minimum that we found for a reliable signal for clustering a bin in MetaBAT, so MetaBAT will ignore anything shorter than that.
Check your data and your assembly... What is the expected metagenome size for your experiment and do you have enough coverage for the assembler to observe at least 10x coverage of the most abundant species?