Usage: sga preprocess [OPTION] --quality-scale=STR READS1 READS2 ...
Prepare READS1, READS2, ... data files for assembly
If pe-mode is turned on (pe-mode=1) then if a read is discarded its pair will be discarded as well.

      --help                           display this help and exit
      -v, --verbose                    display verbose output
      -o, --out=FILE                   write the reads to FILE (default: stdout)
          --phred64                    the input reads are phred64 scaled. They will be converted to phred33.
      -p, --pe-mode=INT                0 - do not treat reads as paired (default)
                                       1 - reads are paired with the first read in READS1 and the second
                                       read in READS2. The paired reads will be interleaved in the output file
                                       2 - reads are paired and the records are interleaved within a single file.
      -q, --quality-trim=INT           perform Heng Li's BWA quality trim algorithm. 
                                       Reads are trimmed according to the formula:
                                       argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT
                                       where l is the original read length.
      -f, --quality-filter=INT         discard the read if it contains more than INT low-quality bases.
                                       Bases with phred score <= 3 are considered low quality. Default: no filtering.
                                       The filtering is applied after trimming so bases removed are not counted.
      -m, --min-length=INT             discard sequences that are shorter than INT
                                       this is most useful when used in conjunction with --quality-trim. Default: 40
      -h, --hard-clip=INT              clip all reads to be length INT. In most cases it is better to use
                                       the soft clip (quality-trim) option.
      --permute-ambiguous              Randomly change ambiguous base calls to one of possible bases.
                                       For example M will be changed to A or C. If this option is not specified, the
                                       entire read will be discarded.
      -s, --sample=FLOAT               Randomly sample reads or pairs with acceptance probability FLOAT.
      --dust                           Perform dust-style filtering of low complexity reads. If you are performing
                                       de novo genome assembly, you probably do not want this.
      --dust-threshold=FLOAT           filter out reads that have a dust score higher than FLOAT (default: 4.0).
                                       This option implies --dust
      --suffix=SUFFIX                  append SUFFIX to each read ID

Report bugs to js18@sanger.ac.uk