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PEAR(1)				  PEAR manual			       PEAR(1)

       PEAR - Paired-end reads merger

       pear [OPTIONS]

       PEAR is a paired-end reads merger for the Illumina platform.

       PEAR  evaluates	all possible paired-end	read overlaps and does not re-
       quire the target	fragment size as input.	It also	implements a statisti-
       cal  test  for  minimizing false-positive results. The highly optimized
       and parallelized	implementation allows for merging millions of  paired-
       end reads within	a few minutes on a standard desktop computer.

       Using  PEAR is very easy. Invoke	it from	the prompt of your command in-
       terpreter as follows:

	   shell> pear -f forward-fastq	-r reverse-fastq -o ouput

       -f, --forward-fastq=FILENAME
	      Forward paired-end FASTQ file

       -r, --reverse-fastq=FILENAME
	      Reverse paired-end FASTQ file

       -o, --output=FILENAME
	      Output filename

       -p, --p-value=PVALUE
	      Specify the value	PVALUE as  the	p-value	 for  the  statistical
	      test.  If	the computer p-value of	a possible merging exceeds the
	      specified	p-value	then the paired-end read will not  be  merged.
	      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=VALUE
	      Set VALUE	as 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  re-
	      duce false-positive assemblies. (default:	10)

       -m, --max-assembly-length=VALUE
	      Set  VALUE  as  the maximum possible length of the assembled se-
	      quences. Setting this value to 0 disables	 the  restriction  and
	      assembled	sequences may be arbitrarily long (default: 0)

       -n, --min-assembly-length=VALUE
	      Set  VALUE  as  the minimum possible length of the assembled se-
	      quences. Setting this value to 0 disables	 the  restriction  and
	      assembled	sequences may be arbitrarily long (default: 0)

       -t, --min-trim-length=VALUE
	      Sets  the	minimum	length of reads	after trimming the low quality
	      part (see	option -q) to VALUE.  (default:	1)

       -q, --quality-threshold=VALUE
	      Sets the quality score threshold for trimming  the  low  quality
	      part  of	a read to VALUE. If the	quality	scores of two consecu-
	      tive bases are strictly less than	the specified  threshold,  the
	      rest of the read will be trimmed.	(default: 0)

       -u, --max-uncalled-base=VALUE
	      Sets  the	 maximal  proportion  of  uncalled  bases in a read to
	      VALUE. Setting this value	to 0 will cause	PEAR  to  discard  all
	      reads  that contain 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=TYPE
	      Specifies	 the  type of statistical test.	Two options are	avail-
	      able, 1 and 2. (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  ex-
	      ample,  setting  the cut-off to 0.05 using this test, the	assem-
	      bled reads might have an actual p-value of 0.02

	      2: Use the acceptance probability	(m.a.p). This test method com-
	      putes 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.	Never-
	      theless,	in  practice, test 2 can correctly assemble more reads
	      with only	slightly higher	false-positive rate  when  the	actual
	      overlap sizes are	relatively small.

       -e, --empirical-freqs
	      Disable empirical	base frequencies. (default: use	empirical base

       -s, --score-method=METHOD
	      Specify the scoring method. Three	options	are  available,	 1,  2
	      and 3. (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

       -b, --phred-base=VALUE
	      Sets the base PHRED quality score	to VALUE. (default: 33)

       -y, --memory=SIZE
	      Specifies	 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. (default:	200M)

       -j, --threads=THREADS
	      Use THREADS number of threads

       -c, --cap=VALUE
	      Specify the upper	bound for the resulting	quality	score. If  set
	      to zero, capping is disabled. (default: 40)

       -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,  with
	      the highest quality score	of the two bases.

       -h, --help This help screen

       Tomas Flouri <>
       Jiajie Zhang <>
       Kassian Kobert <>
       Alexandros Stamatakis <>

       Report PEAR bugs	to

       For  more information, please refer to the PEAR,	which is available on-
       line at

PEAR 0.9.6			  15 Jan 2015			       PEAR(1)


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