soap使用方法

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]

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