# PEAR 0.9.11 ## PEAR - Paired-End reAd mergeR PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer. Location and version: ```console $ which PEAR /local/cluster/bin/PEAR $ PEAR --version PEAR 0.9.11 ``` help message: ```console $ PEAR --help ____ _____ _ ____ | _ \| ____| / \ | _ \ | |_) | _| / _ \ | |_) | | __/| |___ / ___ \| _ < |_| |_____/_/ \_\_| \_\ PEAR v0.9.11 [Nov 5, 2017] - [+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 Standard (mandatory): -f, --forward-fastq Forward paired-end FASTQ file. -r, --reverse-fastq Reverse paired-end FASTQ file. -o, --output Output filename. Optional: -p, --p-value 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 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 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 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 Specify the minimum length of reads after trimming the low quality part (see option -q). (default: 1) -q, --quality-threshold 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 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 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 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 Base PHRED quality score. (default: 33) -y, --memory 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 Specify the upper bound for the resulting quality score. If set to zero, capping is disabled. (default: 40) -j, --threads 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 -k, --keep-original Do not reverse and complement the reverse reads when writing the unassembled and discarded reads output. -i, --stitch concatenate reads by reversing/complementing reverse read -h, --help This help screen. ``` software ref: research ref: