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<code> sh-4.1$ sga assemble --help Usage: sga assemble [OPTION] ... ASQGFILE Create contigs from the assembly graph ASQGFILE. -v, --verbose display verbose output --help display this help and exit -o, --out-prefix=NAME use NAME as the prefix of the output files (output files will be NAME-contigs.fa, etc) -m, --min-overlap=LEN only use overlaps of at least LEN. This can be used to filter the overlap set so that the overlap step only needs to be run once. --transitive-reduction remove transitive edges from the graph. Off by default. --max-edges=N limit each vertex to a maximum of N edges. For highly repetitive regions this helps save memory by culling excessive edges around unresolvable repeats (default: 128) Bubble/Variation removal parameters: -b, --bubble=N perform N bubble removal steps (default: 3) -d, --max-divergence=F only remove variation if the divergence between sequences is less than F (default: 0.05) -g, --max-gap-divergence=F only remove variation if the divergence between sequences when only counting indels is less than F (default: 0.01) Setting this to 0.0 will suppress removing indel variation --max-indel=D do not remove variation that is an indel of length greater than D (default: 20) Trimming parameters: -x, --cut-terminal=N cut off terminal branches in N rounds (default: 10) -l, --min-branch-length=LEN remove terminal branches only if they are less than LEN bases in length (default: 150) Small repeat resolution parameters: -r,--resolve-small=LEN resolve small repeats using spanning overlaps when the difference between the shortest and longest overlap is greater than LEN (default: not performed) Report bugs to js18@sanger.ac.uk sh-4.1$ sga scaffold --help 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. Report bugs to js18@sanger.ac.uk </code>

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archive/scaffold.1429738497.txt.gz · Last modified: 2015/04/22 21:34 by chkan