NAME

       spades - SPAdes genome assembler

SYNOPSIS

       spades [options] -o <output_dir>

DESCRIPTION

       spades is the main executable for the SPAdes software. It assembles genomic reads given to
       it and places the resulting assembly in <output_dir>.

OPTIONS

   Basic options
       -o <output_dir>
           directory to store all the resulting files (required)

       --sc
           this flag is required for MDA (single-cell) data

       --meta
           this flag is required for metagenomic sample data

       --rna
           this flag is required for RNA-seq data

       --plasmid
           runs plasmidSPAdes pipeline for plasmid detection

       --iontorrent
           this flag is required for IonTorrent data

       --test
           runs SPAdes on toy dataset

       -h/--help
           prints this usage message

   Input data
       --12 <filename>
           file with interlaced forward and reverse paired-end reads

       -1 <filename>
           file with forward paired-end reads

       -2 <filename>
           file with reverse paired-end reads

       -s <filename>
           file with unpaired reads

       --pe<#>-12 <filename>
           file with interlaced reads for paired-end library number <#> (<#> = 1,2,3,4,5)

       --pe<#>-1 <filename>
           file with forward reads for paired-end library number <#> (<#> = 1,2,3,4,5)

       --pe<#>-2 <filename>
           file with reverse reads for paired-end library number <#> (<#> = 1,2,3,4,5)

       --pe<#>-s <filename>
           file with unpaired reads for paired-end library number <#> (<#> = 1,2,3,4,5)

       --pe<#>-<or>
           orientation of reads for paired-end library number <#> (<#> = 1,2,3,4,5; <or> = fr,
           rf, ff)

       --s<#> <filename>
           file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)

       --mp<#>-12  <filename>
           file with interlaced reads for mate-pair library number <#> (<#> = 1,2,3,4,5)

       --mp<#>-1 <filename>
           file with forward reads for mate-pair library number <#> (<#> = 1,2,3,4,5)

       --mp<#>-2 <filename>
           file with reverse reads for mate-pair library number <#> (<#> = 1,2,3,4,5)

       --mp<#>-s <filename>
           file with unpaired reads for mate-pair library number <#> (<#> = 1,2,3,4,5)

       --mp<#>-<or>
           orientation of reads for mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf,
           ff)

       --hqmp<#>-12 <filename>
           file with interlaced reads for high-quality mate-pair library number <#> (<#> =
           1,2,3,4,5)

       --hqmp<#>-1 <filename>
           file with forward reads for high-quality mate-pair library number <#> (<#> =
           1,2,3,4,5)

       --hqmp<#>-2 <filename>
           file with reverse reads for high-quality mate-pair library number <#> (<#> =
           1,2,3,4,5)

       --hqmp<#>-s <filename>
           file with unpaired reads for high-quality mate-pair library number <#> (<#> =
           1,2,3,4,5)

       --hqmp<#>-<or>
           orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5;
           <or> = fr, rf, ff)

       --nxmate<#>-1 <filename>
           file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)

       --nxmate<#>-2 <filename>
           file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)

       --sanger <filename>
           file with Sanger reads

       --pacbio <filename>
           file with PacBio reads

       --nanopore <filename>
           file with Nanopore reads

       --trusted-contigs <filename>
           file with trusted contigs

       --untrusted-contigs <filename>
           file with untrusted contigs

   Pipeline options
       --only-error-correction
           runs only read error correction (without assembling)

       --only-assembler
           runs only assembling (without read error correction)

       --careful
           tries to reduce number of mismatches and short indels

       --continue
           continue run from the last available check-point

       --restart-from <cp>
           restart run with updated options and from the specified check-point ('ec', 'as',
           'k<int>', 'mc')

       --disable-gzip-output
           forces error correction not to compress the corrected reads

       --disable-rr
           disables repeat resolution stage of assembling

   Advanced options
       --dataset <filename>
           file with dataset description in YAML format

       -t/--threads <int>
           number of threads [default: 16]

       -m/--memory <int>
           RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]

       --tmp-dir <dirname>
           directory for temporary files [default: <output_dir>/tmp]

       -k <int,int,...>
           comma-separated list of k-mer sizes (must be odd and less than 128) [default: 'auto']

       --cov-cutoff <float>
           coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']

       --phred-offset <33 or 64>
           PHRED quality offset in the input reads (33 or 64) [default: auto-detect]

                                                                                        SPADES(1)