Galaxy |

Pear (version 0.9.6.2)

Dataset type:

Name of file that contains the forward paired-end reads:

-f

Name of file that contains the reverse paired-end reads:

-r

Specify a p-value for the statistical test:

If the computed p-value of a possible assembly exceeds the specified p-value then the paired-end read will not be assembled. Setting 1.0 disables the test. (--p-value)

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. (--min-overlap)

Maximum possible length of the assembled sequences:

Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)

Minimum possible length of the assembled sequences:

Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)

Minimum length of reads after trimming the low quality part:

See option -q. (--min-trim-length)

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. (--quality-threshold)

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. (--max-uncalled-base)

Specify the upper bound for the resulting quality score:

If set to zero, capping is disabled. (--cap)

Type of statistical test:

(--test-method)

Disable empirical base frequencies:

(--empirical-freqs)

Use N base if uncertain:

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. (--nbase)

Scoring method:

(--score-method)

Output files:

What it does

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. 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.

For more information please look at the documentation and github repository.

Please note that PEAR is released under the [CC Attribution-NonCommercial-ShareAlike](https://creativecommons.org/licenses/by-nc-sa/3.0/) license and that commercial partners should obtain a license.