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.