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

                                                                                        SSPACE(1)