'\" t
.\"     Title: spades
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.23
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "SPADES" "1" "" "\ \&" "\ \&"
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.SH "NAME"
spades \- SPAdes genome assembler
.SH "SYNOPSIS"
.sp
\fBspades\fP [options] \-o <output_dir>
.SH "DESCRIPTION"
.sp
\fBspades\fP is the main executable for the \fBSPAdes\fP software. It
assembles genomic reads given to it and places the resulting assembly in
<output_dir>.
.SH "OPTIONS"
.SS "Basic options"
.sp
\fB\-o\fP <output_dir>
.RS 4
directory to store all the resulting files (required)
.RE
.sp
\fB\-\-sc\fP
.RS 4
this flag is required for MDA (single\-cell) data
.RE
.sp
\fB\-\-meta\fP
.RS 4
this flag is required for metagenomic sample data
.RE
.sp
\fB\-\-rna\fP
.RS 4
this flag is required for RNA\-seq data
.RE
.sp
\fB\-\-plasmid\fP
.RS 4
runs plasmidSPAdes pipeline for plasmid detection
.RE
.sp
\fB\-\-iontorrent\fP
.RS 4
this flag is required for IonTorrent data
.RE
.sp
\fB\-\-test\fP
.RS 4
runs SPAdes on toy dataset
.RE
.sp
\fB\-h\fP/\fB\-\-help\fP
.RS 4
prints this usage message
.RE
.SS "Input data"
.sp
\fB\-\-12\fP <filename>
.RS 4
file with interlaced forward and reverse paired\-end reads
.RE
.sp
\fB\-1\fP <filename>
.RS 4
file with forward paired\-end reads
.RE
.sp
\fB\-2\fP <filename>
.RS 4
file with reverse paired\-end reads
.RE
.sp
\fB\-s\fP <filename>
.RS 4
file with unpaired reads
.RE
.sp
\fB\-\-pe<#>\-12\fP <filename>
.RS 4
file with interlaced reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-pe<#>\-1\fP <filename>
.RS 4
file with forward reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-pe<#>\-2\fP <filename>
.RS 4
file with reverse reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-pe<#>\-s\fP <filename>
.RS 4
file with unpaired reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-pe<#>\-<or>\fP
.RS 4
orientation of reads for paired\-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
.RE
.sp
\fB\-\-s<#>\fP <filename>
.RS 4
file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-mp<#>\-12\fP  <filename>
.RS 4
file with interlaced reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-mp<#>\-1\fP <filename>
.RS 4
file with forward reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-mp<#>\-2\fP <filename>
.RS 4
file with reverse reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-mp<#>\-s\fP <filename>
.RS 4
file with unpaired reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-mp<#>\-<or>\fP
.RS 4
orientation of reads for mate\-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
.RE
.sp
\fB\-\-hqmp<#>\-12\fP <filename>
.RS 4
file with interlaced reads for high\-quality mate\-pair library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-hqmp<#>\-1\fP <filename>
.RS 4
file with forward reads for high\-quality mate\-pair library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-hqmp<#>\-2\fP <filename>
.RS 4
file with reverse reads for high\-quality mate\-pair library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-hqmp<#>\-s\fP <filename>
.RS 4
file with unpaired reads for high\-quality mate\-pair library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-hqmp<#>\-<or>\fP
.RS 4
orientation of reads for high\-quality mate\-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
.RE
.sp
\fB\-\-nxmate<#>\-1\fP <filename>
.RS 4
file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-nxmate<#>\-2\fP <filename>
.RS 4
file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
.RE
.sp
\fB\-\-sanger\fP <filename>
.RS 4
file with Sanger reads
.RE
.sp
\fB\-\-pacbio\fP <filename>
.RS 4
file with PacBio reads
.RE
.sp
\fB\-\-nanopore\fP <filename>
.RS 4
file with Nanopore reads
.RE
.sp
\fB\-\-trusted\-contigs\fP <filename>
.RS 4
file with trusted contigs
.RE
.sp
\fB\-\-untrusted\-contigs\fP <filename>
.RS 4
file with untrusted contigs
.RE
.SS "Pipeline options"
.sp
\fB\-\-only\-error\-correction\fP
.RS 4
runs only read error correction (without assembling)
.RE
.sp
\fB\-\-only\-assembler\fP
.RS 4
runs only assembling (without read error correction)
.RE
.sp
\fB\-\-careful\fP
.RS 4
tries to reduce number of mismatches and short indels
.RE
.sp
\fB\-\-continue\fP
.RS 4
continue run from the last available check\-point
.RE
.sp
\fB\-\-restart\-from\fP <cp>
.RS 4
restart run with updated options and from the specified check\-point (\*(Aqec\*(Aq, \*(Aqas\*(Aq, \*(Aqk<int>\*(Aq, \*(Aqmc\*(Aq)
.RE
.sp
\fB\-\-disable\-gzip\-output\fP
.RS 4
forces error correction not to compress the corrected reads
.RE
.sp
\fB\-\-disable\-rr\fP
.RS 4
disables repeat resolution stage of assembling
.RE
.SS "Advanced options"
.sp
\fB\-\-dataset\fP <filename>
.RS 4
file with dataset description in YAML format
.RE
.sp
\fB\-t\fP/\fB\-\-threads\fP <int>
.RS 4
number of threads [default: 16]
.RE
.sp
\fB\-m\fP/\fB\-\-memory\fP <int>
.RS 4
RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]
.RE
.sp
\fB\-\-tmp\-dir\fP <dirname>
.RS 4
directory for temporary files [default: <output_dir>/tmp]
.RE
.sp
\fB\-k\fP <int,int,...>
.RS 4
comma\-separated list of k\-mer sizes (must be odd and less than 128) [default: \*(Aqauto\*(Aq]
.RE
.sp
\fB\-\-cov\-cutoff\fP <float>
.RS 4
coverage cutoff value (a positive float number, or \*(Aqauto\*(Aq, or \*(Aqoff\*(Aq) [default: \*(Aqoff\*(Aq]
.RE
.sp
\fB\-\-phred\-offset\fP <33 or 64>
.RS 4
PHRED quality offset in the input reads (33 or 64) [default: auto\-detect]
.RE