archive:scaffold
Differences
This shows you the differences between two versions of the page.
| Next revision | Previous revision | ||
|
archive:scaffold [2015/04/22 21:34] chkan created |
archive:scaffold [2015/07/18 20:35] (current) ceisenhart ↷ Page moved from scaffold to archive:scaffold |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| <code> | <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 | Usage: scaffold [OPTION] ... [--pe PE-DE] [--mate-pair MATEPAIR-DE] CONTIGSFILE | ||
| Construct scaffolds from CONTIGSFILE using distance estimates. | Construct scaffolds from CONTIGSFILE using distance estimates. | ||
| Line 54: | Line 22: | ||
| be searched for that contains every vertex linked to X. If no such path can be found, the edge of X are removed. | 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. | This builds very conservative scaffolds that should be highly accurate. | ||
| - | |||
| - | Report bugs to js18@sanger.ac.uk | ||
| </code> | </code> | ||
archive/scaffold.1429738497.txt.gz · Last modified: 2015/04/22 21:34 by chkan
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
