[jolespin@campusrocks2 bin]$ ./sga rmdup --help
Usage: sga rmdup [OPTION] ... READFILE
Remove duplicate reads from the data set.

  -v, --verbose                        display verbose output
      --help                           display this help and exit
      -o, --out=FILE                   write the output to FILE (default: READFILE.rmdup.fa)
      -p, --prefix=PREFIX              use PREFIX instead of the prefix of the reads filename for the input/output files
      -e, --error-rate                 the maximum error rate allowed to consider two sequences identical (default: exact matches required)
      -t, --threads=N                  use N threads (default: 1)
      -d, --sample-rate=N              sample the symbol counts every N symbols in the FM-index. Higher values use significantly
                                       less memory at the cost of higher runtime. This value must be a power of 2 (default: 256)

Report bugs to js18@sanger.ac.uk