heguangzhu / megahit

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

MEGAHIT

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. It leverages all available memory (assigned by -m option) to build succinct de Bruijn graphs. CPU-only and GPU-accelerated version of MEGAHIT are provided. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory).

Quick Start

Use CPU-only version of MEGAHIT

% make
% python ./megahit [options] --cpu-only -m <memory_to_use> -l <max_read_len> {-r <reads.fa> | --input_cmd <command>}

Use GPU-accelerated version of MEGAHIT, with a CUDA-enabled GPU and NVCC version 5.5 or higher.

% make use_gpu=1
% python ./megahit [options] -m <memory_to_use> -l <max_read_len> {-r <reads.fa> | --input_cmd <command>}

To show the usage message, type the command

% python ./megahit -h # show the helping manual

Memory control

We recommend to set -m as large as possible, but you should also leave some space for your server. For example, for a server with 64GB free memory, you may try -m 60e9, which is about 56GB. Typically, 56GB memory is quite enough for human guts samples containing 15-30G base-pairs.

Input files

MEGAHIT accepts one fasta or fastq file as input. The input file can be gzip'ed. Alternatively, you can use the option --input-cmd to input reads. Following the --input-cmd should be a command that output all reads to STDOUT in fasta or fastq format. A mix of fasta and fastq is NOT supported. Some correct/wrong examples below.

###Correct examples

• Input from one fastq file named reads.fastq:

-r reads.fastq

• Input from two fasta files sample_1.fa and sample_2.fa:

--input-cmd "cat sample_[12].fa"

• Input from all gzip'ed fastq files in current directory:

--input-cmd "zcat *.fastq.gz"

• Assume fastq-dump is installed, input from a sra file xxx.sra:

--input-cmd "fastq-dump -Z --fasta xxx.sra"

###Wrong examples

• Mixed fastq and fasta files to the input:

--input-cmd "cat *.fa *.fq"

Options

###Choose k MEGAHIT uses multiple k-mer strategy. Minimum k, maximum k and the step for iteration can be set by options --k-min, --k-max and --k-step respectively. k must be odd numbers while the step must be an even number.

###Filter (k_min+1)-mer (k_min+1)-mer with multiplicity lower than d (default 2, assigned by --min-count option) will be discarded. You should be cautious to set d less than 2, which will lead to a much larger and noisy graph. We recommend use the default value 2.

###Mercy k-mer This is specially designed for metagenomics assembly. You can disable this stategy by adding --no-mercy option.

License

  MEGAHIT
  
  Copyright (C) 2014 The University of Hong Kong

  This program is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation, either version 3 of the License, or
  (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program.  If not, see <http://www.gnu.org/licenses/>.