sspace − 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
−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)
Marten Boetzer, Walter Pirovano, Nicola Soranzo