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My current settings are megahit -r input.fq --num-cpu-threads 32 --min-contig-len 300 --presets meta-large -o output. I picked the 'presets meta-large' because I am dealing with a quite large and diverse metagenome out of which I only need some genes.

I've got a contig of interest ~19kb, with a depth of 16. Could I make this contig larger with more relaxed settings? Help would be appreciated!

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You can use the option --k-step 10 and --kmin-1pass for low-coverage datasets.

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