Furthermore, there is an exponential increase in error rates (ERs) along the reads ( Cox et al., 2010). However, single-end reads produced by the Illumina platform typically have a length that ranges from 75 to 300-bp. The deep sequencing capability and low cost of the sequencing-by-synthesis technology is useful for a plethora of applications ranging from whole-genome sequencing ( Liu et al., 2012 Wang et al., 2010) to profiling microbial communities by sequencing the hypervariable regions of the 16S ribosomal RNA (rRNA) gene ( Bartram et al., 2011 Caporaso et al., 2011 Degnan and Ochman, 2012 Rodrigue et al., 2010 Zhou et al., 2011). The Illumina sequencing platform can produce millions of short reads in a single run. On multi-core architectures, the parallel version of PEAR shows linear speedups compared with the sequential version of PEAR.Īvailability and implementation: PEAR is implemented in C and uses POSIX threads. A highly optimized implementation allows for merging millions of paired-end reads within a few minutes on a standard desktop computer. Tests on simulated and empirical data show that PEAR consistently generates highly accurate merged paired-end reads. It also implements a statistical test for minimizing false-positive results. The program evaluates all possible paired-end read overlaps and does not require the target fragment size as input. Results: We present the PEAR software for merging raw Illumina paired-end reads from target fragments of varying length. Therefore, a robust tool is needed to merge paired-end reads that exhibit varying overlap lengths because of varying target fragment lengths. However, when fragment lengths vary and, in particular, when either the fragment size is shorter than a single-end read, or longer than twice the size of a single-end read, most state-of-the-art mergers fail to generate reliable results. There already exist tools for merging these paired-end reads when the target fragments are equally long. Thrown in phar://C:/tools/php/go-pear.phar/PEAR/Start.Motivation: The Illumina paired-end sequencing technology can generate reads from both ends of target DNA fragments, which can subsequently be merged to increase the overall read length. Thrown in phar://C:/tools/php/go-pear.phar/PEAR/Start.php on line 322įatal error: Uncaught Error: Call to undefined method PEAR_Error::set() in phar://C:/tools/php/go-pear.phar/PEAR/Start.php:322 #0 phar://C:/tools/php/go-pear.phar/PEAR/Start/CLI.php(72): PEAR_Start->doInstall() PHP Fatal error: Uncaught Error: Call to undefined method PEAR_Error::set() in phar://C:/tools/php/go-pear.phar/PEAR/Start.php:322 Name of configuration file : C:\tools\php System manual pages directory : C:\tools\php\manġ2. Public Web Files directory : C:\tools\php\wwwġ0. User-modifiable configuration files directory : C:\tools\php\cfgĩ. Documentation directory : C:\tools\php\docsĨ. PHP code directory ($php_dir) : C:\tools\php\pearĦ. Temporary directory for downloads : C:\tools\php\tmpĥ. Temporary directory for processing : C:\tools\php\tmpģ. Installation base ($prefix) : C:\tools\phpĢ. Type 'all' to change all of them or simply press Enter toġ. ToĬhange individual locations, type the number in front of theĭirectory. Name of configuration file : $prefixīelow is a suggested file layout for your new PEAR installation. \go-pear.phar which I got from the official documentation page. Now, I also want to install PEAR but that will output som PHP errors which don't fully know why the happen.īellow the full output of the command php. On a clean Windows installation I installed PHP 7.2 with Nginx which works fine, both via Nginx as on the commandline.
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