Answers.Body: <p>You can use the option <code>--k-step 10</code> and <code>--kmin-1pass</code> for low-coverage datasets.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-20T22:03:54.463Z
Answers.LastActivityDate: 2020-02-20T22:03:54.463Z
Answers.UserDisplayName: zorbax
Body: <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>
  
Tags: <assembly><metagenome>
Title: Can I get longer contigs by changing MEGAHIT settings?
ThreadText: # 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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