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seqclean  

2010-05-28 03:45:23|  分类: 默认分类 |  标签: |举报 |字号 订阅

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seqclean很强大,能去除polya,接头, 载体,此外还可以过滤线粒体序列,核糖体序列等

 seqclean <seqfile> [-v <vecdbs>] [-s <screendbs>] [-r <reportfile>]
    [-o <outfasta>] [-n slicesize] [-c {<num_CPUs>|<PVM_nodefile>}]
    [-l <minlen>] [-N] [-A] [-L] [-x <min_pid>] [-y <min_vechitlen>]
    [-m <e-mail>]
(注 -v 后面的文件须为 formatdb后面的文件名)
Parameters

<seqfile>: sequence file to be analyzed (multi-FASTA)
 
       -c use the specified number of CPUs on local machine
         (default 1) or a list of PVM nodes in <PVM_nodefile>
       -n number of sequences taken at once in each
          search slice (default 2000)
       -v comma delimited list of sequence files
          to use for end-trimming of <seqfile> sequences
          (usually vector sequences)
       -l during cleaning, consider invalid the sequences sorter
          than <minlen> (default 100)
       -s comma delimited list of sequence files to use for
          screening <seqfile> sequences for contamination
          (mito/ribo or different species contamination)
       -r write the cleaning report into file <reportfile>
          (default: <seqfile>.cln)
       -o output the "cleaned" sequences to file <outfasta>
          (default: <seqfile>.clean)
       -x minimum percent identity for an alignemnt with
          a contaminant (default 96)
       -y minimum length of a terminal vector hit to be considered
          (>11, default 11)
       -N disable trimming of ends rich in Ns (undetermined bases)
       -M disable trashing of low quality sequences
       -A disable trimming of polyA/T tails  
       -L disable low-complexity screening (dust)
       -I do not rebuild the cdb index file
       -m send e-mail notifications to <e-mail>
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