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.
-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)
-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)
-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)
-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)
-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