Banana Slug Genomics

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
<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>
Banana Slug Genomics

User Tools

Site Tools

Page Tools
