```bash
pear -h
```

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PEAR v0.9.6 [January 15, 2015]  - [+bzlib +zlib]

Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593

License: Creative Commons Licence
Bug-reports and requests to: Tomas.Flouri@h-its.org and Jiajie.Zhang@h-its.org


Usage: pear <options>
Standard (mandatory):
  -f, --forward-fastq         <str>     Forward paired-end FASTQ file.
  -r, --reverse-fastq         <str>     Reverse paired-end FASTQ file.
  -o, --output                <str>     Output filename.
Optional:
  -p, --p-value               <float>   Specify  a p-value for the statistical test. If the computed
                                        p-value of a possible assembly exceeds the specified p-value
                                        then  paired-end  read  will not be assembled. Valid options
                                        are: 0.0001, 0.001, 0.01, 0.05 and 1.0. Setting 1.0 disables
                                        the test. (default: 0.01)
  -v, --min-overlap           <int>     Specify the minimum overlap size. The minimum overlap may be
                                        set to 1 when the statistical test is used. However, further
                                        restricting  the  minimum overlap size to a proper value may
                                        reduce false-positive assembles. (default: 10)
  -m, --max-assembly-length   <int>     Specify   the  maximum  possible  length  of  the  assembled
                                        sequences.  Setting this value to 0 disables the restriction
                                        and assembled sequences may be arbitrary long. (default: 0)
  -n, --min-assembly-length   <int>     Specify   the  minimum  possible  length  of  the  assembled
                                        sequences.  Setting this value to 0 disables the restriction
                                        and  assembled  sequences  may be arbitrary short. (default:
                                        50)
  -t, --min-trim-length       <int>     Specify  the  minimum length of reads after trimming the low
                                        quality part (see option -q). (default: 1)
  -q, --quality-threshold     <int>     Specify  the  quality  score  threshold for trimming the low
                                        quality  part  of  a  read.  If  the  quality  scores of two
                                        consecutive  bases  are  strictly  less  than  the specified
                                        threshold,  the  rest of the read will be trimmed. (default:
                                        0)
  -u, --max-uncalled-base     <float>   Specify  the maximal proportion of uncalled bases in a read.
                                        Setting this value to 0 will cause PEAR to discard all reads
                                        containing  uncalled  bases.  The other extreme setting is 1
                                        which  causes  PEAR  to process all reads independent on the
                                        number of uncalled bases. (default: 1)
  -g, --test-method           <int>     Specify  the  type  of  statistical  test.  Two  options are
                                        available. (default: 1)
                                        1: Given the minimum allowed overlap, test using the highest
                                        OES. Note that due to its discrete nature, this test usually
                                        yields  a lower p-value for the assembled read than the cut-
                                        off  (specified  by -p). For example, setting the cut-off to
                                        0.05  using  this  test,  the  assembled reads might have an
                                        actual p-value of 0.02.

                                        2. Use the acceptance probability (m.a.p). This test methods
                                        computes  the same probability as test method 1. However, it
                                        assumes  that  the  minimal  overlap is the observed overlap
                                        with  the  highest  OES, instead of the one specified by -v.
                                        Therefore,  this  is  not  a  valid statistical test and the
                                        'p-value'  is  in fact the maximal probability for accepting
                                        the assembly. Nevertheless, we observed in practice that for
                                        the case the actual overlap sizes are relatively small, test
                                        2  can  correctly  assemble  more  reads  with only slightly
                                        higher false-positive rate.
  -e, --empirical-freqs                 Disable  empirical base frequencies. (default: use empirical
                                        base frequencies)
  -s, --score-method          <int>     Specify the scoring method. (default: 2)
                                        1. OES with +1 for match and -1 for mismatch.
                                        2: Assembly score (AS). Use +1 for match and -1 for mismatch
                                        multiplied by base quality scores.
                                        3: Ignore quality scores and use +1 for a match and -1 for a
                                        mismatch.
  -b, --phred-base            <int>     Base PHRED quality score. (default: 33)
  -y, --memory                <str>     Specify  the  amount of memory to be used. The number may be
                                        followed  by  one  of  the  letters  K,  M,  or  G  denoting
                                        Kilobytes,  Megabytes and Gigabytes, respectively. Bytes are
                                        assumed in case no letter is specified.
  -c, --cap                   <int>     Specify  the upper bound for the resulting quality score. If
                                        set to zero, capping is disabled. (default: 40)
  -j, --threads               <int>     Number of threads to use
  -z, --nbase                           When  merging  a  base-pair  that  consists of two non-equal
                                        bases  out  of which none is degenerate, set the merged base
                                        to N and use the highest quality score of the two bases
  -h, --help                            This help screen.