$ sga preprocess --help Usage: sga preprocess [OPTION] 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 --seed set random seed Input/Output options: -o, --out=FILE write the reads to FILE (default: stdout) -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. --pe-orphans=FILE if one half of a read pair fails filtering, write the passed half to FILE Conversions/Filtering: --phred64 convert quality values from phred-64 to phred-33. --discard-quality do not output quality scores -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