Category
Mapping
Usage
soap -a <reads_a> -D <index.files> -o <output></output>
Manual
- -D STR Prefix name for reference index [*.index].
- -a STR Query file, for SE reads alignment or one end of PE reads
- -b STR Query b file, one end of PE reads
- -o STR Output file for alignment results
- -2 STR Output file contains mapped but unpaired reads when do PE alignment
- -u STR Output file for unmapped reads, [none]
- -m INT Minimal insert size INT allowed for PE, [400]
- -x INT Maximal insert size INT allowed for PE, [600]
- -n INT Filter low quality reads contain more INT bp Ns, [5]
- -t Output reads id instead reads name, [none]
- -r INT How to report repeat hits, 0=none; 1=random one; 2=all, [1]
- -R RF alignment for long insert size(>= 2k bps) PE data, [none] FR alignment
- -l INT For long reads with high error rate at 3'-end, those can't align whole length, then first align 5' INT bp subsequence as a seed, [256] use whole length of the read
- -v INT Totally allowed mismatches in one read, [2]
- -M INT Match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]
- 0: exact match only
- 1: 1 mismatch match only
- 2: 2 mismatch match only
- 3: [gap] (coming soon)
- 4: find the best hits
- -p INT Multithreads, n threads, [1]
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