<p>You can use the option <code>--k-step 10</code> and <code>--kmin-1pass</code> for low-coverage datasets.</p>

CC BY-SA 4.0
2020-02-20T22:03:54.463Z
2020-02-20T22:03:54.463Z
zorbax
<p>My current settings are <code>megahit -r input.fq --num-cpu-threads 32 --min-contig-len 300 --presets meta-large -o output</code>. 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.</p>

<p>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!</p>

<assembly><metagenome>
Can I get longer contigs by changing MEGAHIT settings?
# Can I get longer contigs by changing MEGAHIT settings?

(Asked by: username_0 on 2020-02-20)

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!

**Tags:** assembly, metagenome

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## 1 answers

### Answer by username_1 on 2020-02-20. Score: 1 | Accepted answer

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


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