---
name: "sspace"
section: "1"
platform: "linux"
package: "sspace"
version: "2.1.1+dfsg-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sspace"
---

# sspace(1)

SSPACE-basic scaffolding tool

## NAME

sspace - SSPACE-basic scaffolding tool

## SYNOPSIS

**sspace** \[options\] -l \[libraryfilename\]  -s \[contigfilename\]

## DESCRIPTION

SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination.

Please read the README file at /usr/share/doc/sspace/README.gz for more information.

## OPTIONS

### General Parameters

- **-l**

  Library file containing two paired read files with insert size, error and either mate pair or paired end indication (REQUIRED)

- **-s**

  FASTA file containing contig sequences used for extension. Inserted pairs are mapped to extended and non-extended contigs (REQUIRED)

- **-x**

  Indicate whether to extend the contigs of -s using paired reads in -l (-x 1=extension, -x 0=no extension, default -x 0)

### Extension Parameters

- **-m**

  Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 32)

- **-o**

  Minimum number of reads needed to call a base during an extension (default -o 20)

- **-t**

  Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0)

- **-u**

  FASTA/FASTQ file containing unpaired sequence reads (optional)

- **-r**

  Minimum base ratio used to accept a overhang consensus base (default -r 0.9)

### Scaffolding Parameters

- **-z**

  Minimum contig length used for scaffolding. Filters out contigs below this value (default -z 0)

- **-k**

  Minimum number of links (read pairs) to compute scaffold (default -k 5)

- **-a**

  Maximum link ratio between two best contig pairs. **Higher values lead to least accurate scaffolding** (default -a 0.7)

- **-n**

  Minimum overlap required between contigs to merge adjacent contigs in a scaffold (default -n 15)

### Bowtie Parameters

- **-g**

  Maximum number of allowed gaps during mapping with Bowtie. Corresponds to the -v option in Bowtie. Higher number of allowed gaps can lead to least accurate scaffolding. (default -g 0)

- **-T**

  Specify the number of threads in Bowtie. Corresponds to the -p/--threads option in Bowtie (default -T 1)

### Additional Parameters

- **-b**

  Base name for your output files (default -b standard\_output)

- **-v**

  Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0)

- **-p**

  Make .dot file for visualisation (-p 1=yes, -p 0=no, default -p 0)

## AUTHORS

Marten Boetzer, Walter Pirovano, Nicola Soranzo