# sspace(1)

## 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
