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

# megahit\_toolkit(1)

ultra-fast and memory-efficient meta-genome assembler

## NAME

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

## SYNOPSIS

**megahit\_toolkit** *\<sub\_program\>* \[*sub options*\]

## DESCRIPTION

-

  sub-programs:

- assemble

  assemble from SdBG

- local

  local asssembly

- iterate

  extract iterative edges

- buildlib

  build read library

- count

  kmer counting

- read2sdbg

  build sdbg from reads

- seq2sdbg

  build sdbg from megahit contigs + edges

- contig2fastg

  convert MEGAHIT's k\*.contigs.fa to fastg format

- readstat

  calculate read stats (# of reads, bases, longest, shortest, average)

- filterbylen

  filter contigs by length

- checkcpu

  check whether the run-time CPU supports POPCNT and BMI2

- checkpopcnt

  check whether the run-time CPU supports POPCNT

- checkbmi2

  check whether the run-time CPU supports BMI2

- dumpversion

  dump version

- kmax

  the largest k value supported

## AUTHOR

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