Provided by: sspace_2.1.1+dfsg-4_all
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 SSPACE(1)