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 sequence graph from FILE. This supercedes --contig-file --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 --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