.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH MEGAHIT "1" "October 2019" "megahit 1.2.8" "User Commands"
.SH NAME
megahit \- ultra-fast and memory-efficient meta-genome assembler
.SH DESCRIPTION
MEGAHIT v1.2.8
.PP
contact: Dinghua Li <voutcn@gmail.com>
.SS "Usage:"
.IP
megahit [options] {\-1 <pe1> \fB\-2\fR <pe2> | \fB\-\-12\fR <pe12> | \fB\-r\fR <se>} [\-o <out_dir>]
.IP
Input options that can be specified for multiple times (supporting plain text and gz/bz2 extensions)
.TP
\fB\-1\fR
<pe1>          comma\-separated list of fasta/q paired\-end #1 files, paired with files in <pe2>
.TP
\fB\-2\fR
<pe2>          comma\-separated list of fasta/q paired\-end #2 files, paired with files in <pe1>
.TP
\fB\-\-12\fR
<pe12>         comma\-separated list of interleaved fasta/q paired\-end files
.TP
\fB\-r\fR/\-\-read
<se>           comma\-separated list of fasta/q single\-end files
.SS "Optional Arguments:"
.IP
Basic assembly options:
.TP
\fB\-\-min\-count\fR
<int>          minimum multiplicity for filtering (k_min+1)\-mers [2]
.TP
\fB\-\-k\-list\fR
<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]
.IP
Another way to set \fB\-\-k\-list\fR (overrides \fB\-\-k\-list\fR if one of them set):
.TP
\fB\-\-k\-min\fR
<int>          minimum kmer size (<= 255), must be odd number [21]
.TP
\fB\-\-k\-max\fR
<int>          maximum kmer size (<= 255), must be odd number [141]
.TP
\fB\-\-k\-step\fR
<int>          increment of kmer size of each iteration (<= 28), must be even number [12]
.IP
Advanced assembly options:
.TP
\fB\-\-no\-mercy\fR
do not add mercy kmers
.TP
\fB\-\-bubble\-level\fR
<int>          intensity of bubble merging (0\-2), 0 to disable [2]
.TP
\fB\-\-merge\-level\fR
<l,s>          merge complex bubbles of length <= l*kmer_size and similarity >= s [20,0.95]
.TP
\fB\-\-prune\-level\fR
<int>          strength of low depth pruning (0\-3) [2]
.TP
\fB\-\-prune\-depth\fR
<int>          remove unitigs with avg kmer depth less than this value [2]
.TP
\fB\-\-disconnect\-ratio\fR
<float>        disconnect unitigs if its depth is less than this ratio times
the total depth of itself and its siblings [0.1]
.TP
\fB\-\-low\-local\-ratio\fR
<float>        remove unitigs if its depth is less than this ratio times
the average depth of the neighborhoods [0.2]
.TP
\fB\-\-max\-tip\-len\fR
<int>          remove tips less than this value [2*k]
.TP
\fB\-\-cleaning\-rounds\fR
<int>          number of rounds for graph cleanning [5]
.TP
\fB\-\-no\-local\fR
disable local assembly
.TP
\fB\-\-kmin\-1pass\fR
use 1pass mode to build SdBG of k_min
.IP
Presets parameters:
.TP
\fB\-\-presets\fR
<str>          override a group of parameters; possible values:
meta\-sensitive: '\-\-min\-count 1 \fB\-\-k\-list\fR 21,29,39,49,...,129,141'
meta\-large: '\-\-k\-min 27 \fB\-\-k\-max\fR 127 \fB\-\-k\-step\fR 10'
(large & complex metagenomes, like soil)
.IP
Hardware options:
.TP
\fB\-m\fR/\-\-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]
.TP
\fB\-\-mem\-flag\fR
<int>          SdBG builder memory mode. 0: minimum; 1: moderate;
others: use all memory specified by '\-m/\-\-memory' [1]
.TP
\fB\-t\fR/\-\-num\-cpu\-threads
<int>          number of CPU threads [# of logical processors]
.TP
\fB\-\-no\-hw\-accel\fR
run MEGAHIT without BMI2 and POPCNT hardware instructions
.IP
Output options:
.TP
\fB\-o\fR/\-\-out\-dir
<string>       output directory [./megahit_out]
.TP
\fB\-\-out\-prefix\fR
<string>       output prefix (the contig file will be OUT_DIR/OUT_PREFIX.contigs.fa)
.TP
\fB\-\-min\-contig\-len\fR
<int>          minimum length of contigs to output [200]
.TP
\fB\-\-keep\-tmp\-files\fR
keep all temporary files
.TP
\fB\-\-tmp\-dir\fR
<string>       set temp directory
.SS "Other Arguments:"
.TP
\fB\-\-continue\fR
continue a MEGAHIT run from its last available check point.
please set the output directory correctly when using this option.
.TP
\fB\-\-test\fR
run MEGAHIT on a toy test dataset
.TP
\fB\-h\fR/\-\-help
print the usage message
.TP
\fB\-v\fR/\-\-version
print version
.SH AUTHOR
This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.