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SSPACE

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

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