Banana Slug Genomics

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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.

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Banana Slug Genomics

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