---
name: "spades"
section: "1"
platform: "linux"
package: "spades"
version: "4.0.0+really3.15.5+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/spades"
---

# spades(1)

SPAdes genome assembler

## 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) \[default: auto-detect\]