sspace(1) SSPACE-basic scaffolding tool


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


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.


General Parameters


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


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


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


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


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


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


FASTA/FASTQ file containing unpaired sequence reads (optional)


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

Scaffolding Parameters


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


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


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


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

Bowtie Parameters


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)


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

Additional Parameters


Base name for your output files (default -b standard_output)


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


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


Marten Boetzer, Walter Pirovano, Nicola Soranzo