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.

megahit 1.2.8                                     October 2019                                        MEGAHIT(1)