SPADES

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]