---
name: "dipspades"
section: "1"
platform: "linux"
package: "spades"
version: "3.9.1+dfsg-1"
release: "Debian 9 (Stretch)"
platforms: ["linux"]
url: "https://new.carta.tech/dipspades"
---

# dipspades(1)

diploid genome assembler

## NAME

dipspades - diploid genome assembler

## SYNOPSIS

**dipspades** \[options\] -o \<output\_dir\>

## DESCRIPTION

**dipspades** is the main executable for the **dipSPAdes** software, a genome assembler designed for diploid genomes with a high heterozygosity rate. 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)

- **--iontorrent**

  this flag is required for IonTorrent data

- **--test**

  runs dipSPAdes 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

### Input haplocontigs

- **--hap** \<filename\>

  file with haplocontigs

### Pipeline options

- **--only-assembler**

  runs only assembling (without read error correction)

- **--disable-gzip-output**

  forces error correction not to compress the corrected reads

- **--disable-rr**

  disables repeat resolution stage of assembling

### dipSPAdes options

- **--expect-gaps**

  indicates that significant number of gaps in coverage is expected

- **--expect-rearrangements**

  indicates that significant number of rearrangements between haplomes of diploid genome is expected

- **--hap-assembly**

  enables haplotype assembly phase

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