spades.py(1) · carta

Usage

spades [options] -o <output_dir>

Overview

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]

History

Debian 13 (Trixie): the text shown here
Debian 12 (Bookworm)
Debian 11 (Bullseye)
Debian 10 (Buster)
Debian 9 (Stretch)