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