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Usage: scaffold2fasta [OPTION] ... [-f CONTIGSFILE | -a ASQGFILE] SCAFFOLDFILE
Write out a fasta file for the scaffolds indicated in SCAFFOLDFILE
One of -f CONTIGSFILE or -a ASQGFILE must be provided. If an asqg file is provided,
the program can attempt to determine the sequence linking the scaffold components by
walking the graph/

      --help                           display this help and exit
      -v, --verbose                    display verbose output
      -f, --contig-file=FILE           read the contig sequences from FILE
      -a, --asqg-file=FILE             read the contig string graph from FILE. This supercedes --contig-file
                                       this is usually the output from the sga-assemble step
          --no-singletons              do not output scaffolds that consist of a single contig
      -o, --outfile=FILE               write the scaffolds to FILE (default: scaffolds.fa)
      -m, --min-length=N               only output scaffolds longer than N bases
          --write-unplaced             output unplaced contigs that are larger than minLength
          --write-names                write the name of contigs contained in the scaffold in the FASTA header
          --min-gap-length=N           separate contigs by at least N bases. All predicted gaps less
                                       than N will be extended to N (default: 25)
          --use-overlap                attempt to merge contigs using predicted overlaps.
                                       This can help close gaps in the scaffolds but comes
                                       with a small risk of collapsing tandem repeats.
      -g, --graph-resolve=MODE         if an ASQG file is present, attempt to resolve the links
                                       between contigs using walks through the graph. The MODE parameter
                                       is a string describing the algorithm to use.
                                       The MODE parameter must be one of best-any|best-unique|unique|none.
                                       best-any: The walk with length closest to the estimated
                                       distance between the contigs will be chosen to resolve the gap.
                                       If multiple best walks are found, the tie is broken arbitrarily.
                                       best-unique: as above but if there is a tie no walk will be chosen.
                                       unique: only resolve the gap if there is a single walk between the contigs
                                       none: do not resolve gaps using the graph
                                       The most conservative most is unique, then best-unique with best-any being the most
                                       aggressive. The default is unique
      -d, --distanceFactor=T           Accept a walk as correctly resolving a gap if the walk length is within T standard
                                       deviations from the estimated distance (default: 3.0f)

Report bugs to js18@sanger.ac.uk

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