# MEGAHIT 1.2.9


MEGAHIT
=======

MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized
for metagenomes, but also works well on generic single genome assembly (small
or mammalian size) and single-cell assembly.

Usage
-----

### Basic usage
```sh
megahit -1 pe_1.fq -2 pe_2.fq -o out  # 1 paired-end library
megahit --12 interleaved.fq -o out # one paired & interleaved paired-end library
megahit -1 a1.fq,b1.fq,c1.fq -2 a2.fq,b2.fq,c2.fq -r se1.fq,se2.fq -o out # 3 paired-end libraries + 2 SE libraries
megahit_core contig2fastg 119 out/intermediate_contigs/k119.contig.fa > k119.fastg # get FASTG from the intermediate contigs of k=119
```
The contigs can be found `final.contigs.fa` in the output directory.

### Advanced usage
* `--kmin-1pass`: if sequencing depth is low and too much memory used when
  build the graph of k_min
* `--presets meta-large`: if the metagenome is complex (i.e., bio-diversity is
  high, for example soil metagenomes)
* `--cleaning-rounds 1 --disconnect-ratio 0`: get less pruned assembly
  (usually shorter contigs)
* `--continue -o out`: resume an interrupted job from `out`

To see the full manual, run `megahit` without parameters or with `-h`.

Also, our [wiki](https://github.com/voutcn/megahit/wiki) may be helpful.

Location and version:

```console
$ which megahit
/local/cluster/bin/megahit
$ megahit --version
MEGAHIT v1.2.9
```

help message:

```console
$ megahit --help
MEGAHIT v1.2.9

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 filesin <pe2>
    -2                       <pe2>          comma-separated list of fasta/q paired-end #2 files, paired with filesin <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
```

software ref: <https://github.com/voutcn/megahit>  
research ref: <https://doi.org/10.1093/bioinformatics/btv033>