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