Manpages. Will refine the outputs soon

debian/mans/*.1

.\" 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.

.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.

.TH MEGAHIT_CORE "1" "October 2019" "megahit_core 1.2.8" "User Commands"

.SH NAME

megahit_core \- ultra-fast and memory-efficient meta-genome assembler

.SH SYNOPSIS

.B megahit_core

\fI\,<sub_program> \/\fR[\fI\,sub options\/\fR]

.SH DESCRIPTION

.IP

sub\-programs:

.TP

assemble

assemble from SdBG

.TP

local

local asssembly

.TP

iterate

extract iterative edges

.TP

buildlib

build read library

.TP

count

kmer counting

.TP

read2sdbg

build sdbg from reads

.TP

seq2sdbg

build sdbg from megahit contigs + edges

.TP

contig2fastg

convert MEGAHIT's k*.contigs.fa to fastg format

.TP

readstat

calculate read stats (# of reads, bases, longest, shortest, average)

.TP

filterbylen

filter contigs by length

.TP

checkcpu

check whether the run\-time CPU supports POPCNT and BMI2

.TP

checkpopcnt

check whether the run\-time CPU supports POPCNT

.TP

checkbmi2

check whether the run\-time CPU supports BMI2

.TP

dumpversion

dump version

.TP

kmax

the largest k value supported

.SH AUTHOR

This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.

.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.

.TH MEGAHIT_CORE_NO_HW_ACCEL "1" "October 2019" "megahit_core_no_hw_accel 1.2.8" "User Commands"

.SH NAME

megahit_core_no_hw_accel \- ultra-fast and memory-efficient meta-genome assembler

.SH SYNOPSIS

.B megahit_core_no_hw_accel

\fI\,<sub_program> \/\fR[\fI\,sub options\/\fR]

.SH DESCRIPTION

.IP

sub\-programs:

.TP

assemble

assemble from SdBG

.TP

local

local asssembly

.TP

iterate

extract iterative edges

.TP

buildlib

build read library

.TP

count

kmer counting

.TP

read2sdbg

build sdbg from reads

.TP

seq2sdbg

build sdbg from megahit contigs + edges

.TP

contig2fastg

convert MEGAHIT's k*.contigs.fa to fastg format

.TP

readstat

calculate read stats (# of reads, bases, longest, shortest, average)

.TP

filterbylen

filter contigs by length

.TP

checkcpu

check whether the run\-time CPU supports POPCNT and BMI2

.TP

checkpopcnt

check whether the run\-time CPU supports POPCNT

.TP

checkbmi2

check whether the run\-time CPU supports BMI2

.TP

dumpversion

dump version

.TP

kmax

the largest k value supported

.SH AUTHOR

This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.

.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.

.TH MEGAHIT_CORE_POPCNT "1" "October 2019" "megahit_core_popcnt 1.2.8" "User Commands"

.SH NAME

megahit_core_popcnt \- ultra-fast and memory-efficient meta-genome assembler

.SH SYNOPSIS

.B megahit_core_popcnt

\fI\,<sub_program> \/\fR[\fI\,sub options\/\fR]

.SH DESCRIPTION

.IP

sub\-programs:

.TP

assemble

assemble from SdBG

.TP

local

local asssembly

.TP

iterate

extract iterative edges

.TP

buildlib

build read library

.TP

count

kmer counting

.TP

read2sdbg

build sdbg from reads

.TP

seq2sdbg

build sdbg from megahit contigs + edges

.TP

contig2fastg

convert MEGAHIT's k*.contigs.fa to fastg format

.TP

readstat

calculate read stats (# of reads, bases, longest, shortest, average)

.TP

filterbylen

filter contigs by length

.TP

checkcpu

check whether the run\-time CPU supports POPCNT and BMI2

.TP

checkpopcnt

check whether the run\-time CPU supports POPCNT

.TP

checkbmi2

check whether the run\-time CPU supports BMI2

.TP

dumpversion

dump version

.TP

kmax

the largest k value supported

.SH AUTHOR

This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.