Usage:  soap [options]

       -a  <str>   query a file, *.fq or *.fa format

       -d  <str>   reference sequences file, *.fa format

       -o  <str>   output alignment file

       -s  <int>   seed size, default=10. [read>18,s=8; read>22,s=10, read>26, s=12]

       -v  <int>   maximum number of mismatches allowed on a read, <=5. default=2bp. For pair-ended alignment, this version will allow either 0 or 2 mismatches.

       -g  <int>   maximum gap size allowed on a read, default=0bp

       -w  <int>   maximum number of equal best hits to count, smaller will be faster, <=10000

       -e  <int>   will not allow gap exist inside n-bp edge of a read, default=5bp

       -z  <char>  initial quality, default=@ [Illumina is using '@', Sanger Institute is using '!']

       -c  <int>   how to trim low-quality at 3-end?

                   0:     don't trim;

                   1-10:  trim n-bps at 3-end for all reads;

                   11-20: trim first bp and (n-10)-bp at 3-end for all reads;

                   21-30: trim (n-20)-bp at 3-end and redo alignment if the original read have no hit;

                   31-40: trim first bp and (n-30)-bp at 3-end and redo alignment if the original read have no hit;

                   41-50: iteratively trim (n-40)-bp at 3-end until getting hits;

                   51-60: if no hit, trim first bp and iteratively trim (n-50)bp at 3-end until getting hits;

                   default: 0

       -f  <int>   filter low-quality reads containing >n Ns, default=5

       -r  [0,1,2] how to report repeat hits, 0=none; 1=random one; 2=all, default=1

       -t          read ID in output file, [name, order in input file], default: name

       -n  <int>   do alignment on which reference chain? 0:both; 1:forward only; 2:reverse only. default=0

       -p  <int>   number of processors to use, default=1

  Options for pair-end alignment:

       -b  <str>   query b file

       -m  <int>   minimal insert size allowed, default=400

       -x  <int>   maximal insert size allowed, default=600

       -2  <str>   output file of unpaired alignment hits

       -y          do not optimize for SV analysis, default will output hit a and hit b with smallest distance in unpaired alignment

  Options for mRNA tag alignment:

       -T  <int>   type of tag, 0:DpnII, GATC+16; 1:NlaIII, CATG+17. default=-1[not mRNA tag]

  Options for miRNA alignment:

       -A  <str>   3-end adapter sequence, default=[not miRNA]

       -S  <int>   number of mismatch allowed in adapter, default=0

       -M  <int>   minimum length of a miRNA, default=17

       -X  <int>   maximum length of a miRNA, default=26

       -h          help

Command lines:

   single-end alignment: soap -a query.fa -d ref.fa -o out.sop -s 12

   pair-end alignment:   soap -a query_1.fa -b query_2.fa -d ref.fa -o out.sop -2 single.sop -m 100 -x 150

   batch model:          soap -d ref.fa <parameter file>

      SOAP provides batch model for alignment of multiple query datasets onto the same reference, which will avoid loading reference and constructing indexing hash for multiple times. the <parameter file> contains options for each query:

      <parameter file>:

      -a q1.fa -o out1.sop -s 12

      -a q2.fa -o out2.sop -s 12

      ...

      -a qn.fa -o outn.sop -s 10

Note: location coordinates are counted from 1

Setting seed size: seed_size*2+3<=min_read_size, AND seed_size<=12

Output format:

  id, seq, qual, #_of_hits, a/b[belonging to query a or b if pair-end], length, +/-, ref, ref_location, type

  Types:

    0:                  exact match;

    n OffsetAlleleQual: n mismatches with offset, allele and quality, ex: 1 C->10T30, 1-bp mismatch at location+10 on ref, ref allele C, query allele T, query quality 30;

    100+n Offset:       n-bp insertion on query, ex: 101 15, 1-bp insertion on query, start after 15bp on ref

    200+n Offset:       n-bp deletion on query, ex: 201 16, 1-bp deletion on query, start after 16bp on ref

文章来源：http://blog.163.com/henry_by/blog/static/5726535820100288482842/