NAME

SYNOPSIS

DESCRIPTION

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 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 interpreter 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 restricting 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 sequences 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 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 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 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 method 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, 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 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

BUGS

SEE ALSO