SeqPrep

Description

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SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap. When an adapter sequence is present, that means that the two reads must overlap (in most cases) so they are forcefully merged. When reads do not have adapter sequence they must be treated with care when doing the merging, so a much more sensitive approach is taken. The default parameters were chosen with sensitivity in mind, so that they could be ran on libraries where very few reads are expected to overlap. It is always safest though to save the overlapping procedure for libraries where you have some prior knowledge that a significant portion of the reads will have some overlap. Template:App Location

Available versions

• 0.4
• 0.5 (EL6), small changes that don't affect the functionality.

Running the application using modules

To use seqprep with the environment modules system at HPC the following commands are available:

Get module information for seqprep:

$module spider seqprep

Load the default application module:

$module load seqprep

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_SEQPREP_DIR - directory where seqprep is located.