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<code> Usage: scaffold [OPTION] ... [--pe PE-DE] [--mate-pair MATEPAIR-DE] CONTIGSFILE Construct scaffolds from CONTIGSFILE using distance estimates. The distance estimates are read from the --pe and --matepair parameters --help display this help and exit -v, --verbose display verbose output --pe=FILE load links derived from paired-end (short insert) libraries from FILE --mate-pair=FILE load links derived from mate-pair (long insert) libraries from FILE -m, --min-length=N only use contigs at least N bp in length to build scaffolds (default: no minimun). -g, --asqg-file=FILE optionally load the sequence graph from FILE -a, --astatistic-file=FILE load Myers' A-statistic values from FILE. This is used to determine unique and repetitive contigs with the -u/--unique-astat and -r/--repeat-astat parameters (required) -u, --unique-astat=FLOAT Contigs with an a-statitic value about FLOAT will be considered unique (default: 20.0) -c, --min-copy-number=FLOAT remove vertices with estimated copy number less than FLOAT (default: 0.5f) -s, --max-sv-size=N collapse heterozygous structural variation if the event size is less than N (default: 0) -o, --outfile=FILE write the scaffolds to FILE (default: CONTIGSFILE.scaf --remove-conflicting if two contigs have multiple distance estimates between them and they do not agree, break the scaffold at this point --strict perform strict consistency checks on the scaffold links. If a vertex X has multiple edges, a path will be searched for that contains every vertex linked to X. If no such path can be found, the edge of X are removed. This builds very conservative scaffolds that should be highly accurate. </code>
