# FreeBSD Manual Pages

PEAR(1) PEAR manual PEAR(1)NAMEPEAR - Paired-end reads mergerSYNOPSISpear[OPTIONS]DESCRIPTIONPEARis a paired-end reads merger for the Illumina platform.PEARevaluates 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. UsingPEARis very easy. Invoke it from the prompt of your command in- terpreter as follows: shell>pear-fforward-fastq-rreverse-fastq-oouputOPTIONS-f,--forward-fastq=FILENAMEForward paired-end FASTQ file-r,--reverse-fastq=FILENAMEReverse paired-end FASTQ file-o,--output=FILENAMEOutput filename-p,--p-value=PVALUESpecify the valuePVALUEas 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:0.0001,0.001,0.01,0.05and1.0. Setting1.0disables the test. (default:0.01)-v,--min-overlap=VALUESetVALUEas the minimum overlap size. The minimum overlap may be set to1when 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=VALUESetVALUEas the maximum possible length of the assembled se- quences. Setting this value to0disables the restriction and assembled sequences may be arbitrarily long (default:0)-n,--min-assembly-length=VALUESetVALUEas the minimum possible length of the assembled se- quences. Setting this value to0disables the restriction and assembled sequences may be arbitrarily long (default:0)-t,--min-trim-length=VALUESets the minimum length of reads after trimming the low quality part (see option-q) toVALUE. (default:1)-q,--quality-threshold=VALUESets the quality score threshold for trimming the low quality part of a read toVALUE. 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=VALUESets the maximal proportion of uncalled bases in a read toVALUE. Setting this value to0will causePEARto discard all reads that contain uncalled bases. The other extreme setting is1which causesPEARto process all reads independent on the number of uncalled bases. (default:1)-g,--test-method=TYPESpecifies the type of statistical test. Two options are avail- able,1and2. (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 to0.05using this test, the assem- bled reads might have an actual p-value of0.022: Use the acceptance probability (m.a.p). This test method com- putes the same probability as test method1. 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, test2can correctly assemble more reads with only slightly higher false-positive rate when the actual overlap sizes are relatively small.-e,--empirical-freqsDisable empirical base frequencies. (default: use empirical base frequencies)-s,--score-method=METHODSpecify the scoring method. Three options are available,1,2and3. (default:2)1: OES with +1 for match and -1 for mismatch2: Assembly score (AS). Use +1 for match and -1 for mismatch multiplied by base quality scores3: Ignore quality scores and use +1 for a match and -1 for a mismatch-b,--phred-base=VALUESets the base PHRED quality score toVALUE. (default:33)-y,--memory=SIZESpecifies the amount of memory to be used. The number may be followed by one of the lettersK,M, orGdenoting Kilobytes, Megabytes and Gigabytes, respectively. Bytes are assumed in case no letter is specified. (default:200M)-j,--threads=THREADSUseTHREADSnumber of threads-c,--cap=VALUESpecify the upper bound for the resulting quality score. If set to zero, capping is disabled. (default:40)-z,--nbaseWhen merging a base-pair that consists of two non equal bases out of which none is degenerate, set the merged base toN, with the highest quality score of the two bases.-h,--helpThis help screenAUTHORSTomasFlouri<Tomas.Flouri@h-its.org>JiajieZhang<Jiajie.Zhang@h-its.org>KassianKobert<Kassian.Kobert@h-its.org>AlexandrosStamatakis<Alexandros.Stamatakis@h-its.org>BUGSReportPEARbugs topear-users@googlegroups.comSEE ALSOFor more information, please refer to thePEAR, which is available on- line athttp://www.exelixis-lab.org/web/software/pearPEAR 0.9.6 15 Jan 2015 PEAR(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHORS | BUGS | SEE ALSO

Want to link to this manual page? Use this URL:

<https://www.freebsd.org/cgi/man.cgi?query=pearRM&sektion=1&manpath=FreeBSD+12.2-RELEASE+and+Ports>