---
name: "megahit"
section: "1"
platform: "linux"
package: "megahit"
version: "1.2.9-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/megahit"
---

# megahit(1)

ultra-fast and memory-efficient meta-genome assembler

## NAME

megahit - ultra-fast and memory-efficient meta-genome assembler

## DESCRIPTION

MEGAHIT v1.2.8

contact: Dinghua Li \<voutcn@gmail.com\>

### Usage:

-

  megahit \[options\] {-1 \<pe1\> **-2** \<pe2\> \| **--12** \<pe12\> \| **-r** \<se\>} \[-o \<out\_dir\>\]

-

  Input options that can be specified for multiple times (supporting plain text and gz/bz2 extensions)

- **-1**

  \<pe1\>          comma-separated list of fasta/q paired-end #1 files, paired with files in \<pe2\>

- **-2**

  \<pe2\>          comma-separated list of fasta/q paired-end #2 files, paired with files in \<pe1\>

- **--12**

  \<pe12\>         comma-separated list of interleaved fasta/q paired-end files

- **-r**/--read

  \<se\>           comma-separated list of fasta/q single-end files

### Optional Arguments:

-

  Basic assembly options:

- **--min-count**

  \<int\>          minimum multiplicity for filtering (k\_min+1)-mers \[2\]

- **--k-list**

  \<int,int,..\>   comma-separated list of kmer size all must be odd, in the range 15-255, increment \<= 28) \[21,29,39,59,79,99,119,141\]

-

  Another way to set **--k-list** (overrides **--k-list** if one of them set):

- **--k-min**

  \<int\>          minimum kmer size (\<= 255), must be odd number \[21\]

- **--k-max**

  \<int\>          maximum kmer size (\<= 255), must be odd number \[141\]

- **--k-step**

  \<int\>          increment of kmer size of each iteration (\<= 28), must be even number \[12\]

-

  Advanced assembly options:

- **--no-mercy**

  do not add mercy kmers

- **--bubble-level**

  \<int\>          intensity of bubble merging (0-2), 0 to disable \[2\]

- **--merge-level**

  \<l,s\>          merge complex bubbles of length \<= l\*kmer\_size and similarity \>= s \[20,0.95\]

- **--prune-level**

  \<int\>          strength of low depth pruning (0-3) \[2\]

- **--prune-depth**

  \<int\>          remove unitigs with avg kmer depth less than this value \[2\]

- **--disconnect-ratio**

  \<float\>        disconnect unitigs if its depth is less than this ratio times the total depth of itself and its siblings \[0.1\]

- **--low-local-ratio**

  \<float\>        remove unitigs if its depth is less than this ratio times the average depth of the neighborhoods \[0.2\]

- **--max-tip-len**

  \<int\>          remove tips less than this value \[2\*k\]

- **--cleaning-rounds**

  \<int\>          number of rounds for graph cleanning \[5\]

- **--no-local**

  disable local assembly

- **--kmin-1pass**

  use 1pass mode to build SdBG of k\_min

-

  Presets parameters:

- **--presets**

  \<str\>          override a group of parameters; possible values: meta-sensitive: '--min-count 1 **--k-list** 21,29,39,49,...,129,141' meta-large: '--k-min 27 **--k-max** 127 **--k-step** 10' (large & complex metagenomes, like soil)

-

  Hardware options:

- **-m**/--memory

  \<float\>        max memory in byte to be used in SdBG construction (if set between 0-1, fraction of the machine's total memory) \[0.9\]

- **--mem-flag**

  \<int\>          SdBG builder memory mode. 0: minimum; 1: moderate; others: use all memory specified by '-m/--memory' \[1\]

- **-t**/--num-cpu-threads

  \<int\>          number of CPU threads \[# of logical processors\]

- **--no-hw-accel**

  run MEGAHIT without BMI2 and POPCNT hardware instructions

-

  Output options:

- **-o**/--out-dir

  \<string\>       output directory \[./megahit\_out\]

- **--out-prefix**

  \<string\>       output prefix (the contig file will be OUT\_DIR/OUT\_PREFIX.contigs.fa)

- **--min-contig-len**

  \<int\>          minimum length of contigs to output \[200\]

- **--keep-tmp-files**

  keep all temporary files

- **--tmp-dir**

  \<string\>       set temp directory

### Other Arguments:

- **--continue**

  continue a MEGAHIT run from its last available check point. please set the output directory correctly when using this option.

- **--test**

  run MEGAHIT on a toy test dataset

- **-h**/--help

  print the usage message

- **-v**/--version

  print version

## AUTHOR

This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.