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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

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