#################################################################### sga preprocess --help 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