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PEAR(1) PEAR manual PEAR(1) NAME PEAR - Paired-end reads merger SYNOPSIS pear [OPTIONS] DESCRIPTION PEAR is a paired-end reads merger for the Illumina platform. PEAR evaluates all possible paired-end read overlaps and does not require the target fragment size as input. It also implements a statistical test for minimizing false-positive results. The highly optimized and paral- lelized 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 inter- preter as follows: shell> pear -f forward-fastq -r reverse-fastq -o ouput OPTIONS -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 re- stricting the minimum overlap size to a proper value may reduce false-positive assemblies. (default: 10) -m, --max-assembly-length=VALUE Set VALUE as the maximum possible length of the assembled sequences. Setting this value to 0 disables the restriction and assembled se- quences may be arbitrarily long (default: 0) -n, --min-assembly-length=VALUE Set VALUE as the minimum possible length of the assembled sequences. Setting this value to 0 disables the restriction and assembled se- quences 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 consecutive 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 available, 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 computes the same probability as test method 1. However, it assumes that the minimal overlap is the observed over- lap 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 ac- cepting the assembly. Nevertheless, 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 empiri- cal base frequencies) -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 mismatch -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 AUTHORS Tomas Flouri <Tomas.Flouri@h-its.org> Jiajie Zhang <Jiajie.Zhang@h-its.org> Kassian Kobert <Kassian.Kobert@h-its.org> Alexandros Stamatakis <Alexandros.Stamatakis@h-its.org> BUGS Report PEAR bugs to pear-users@googlegroups.com SEE ALSO For more information, please refer to the PEAR, which is available online at http://www.exelixis-lab.org/web/software/pear PEAR 0.9.6 15 Jan 2015 PEAR(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHORS | BUGS | SEE ALSO
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