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Filter Out Low-Complexity Reads with PRINSEQ - v0.20.4


By: jkbaumohl


Filter out low-complexity paired- or single-end reads with PRINSEQ.

This App filters low-complexity reads from single- or paired-end read libraries using PRINSEQ. There are two filtering methods to choose from (i) Dust and (ii) Entropy. Note that the Entropy threshold becomes more strict as the threshold value increases, whereas the Dust threshold becomes more strict as the threshold decreases. The threshold value field used is determined by the Filtering Method selected.

If the input reads object is a SingleEndLibrary, the resulting object will be a filtered SingleEndLibrary object. If the input reads object is a PairedEndLibrary, however, there is the potential for the following 3 objects to be made:

Output Report:

The output first lists the objects created within KBase as a result of running PRINSEQ.

The next section of the output details summary statistics of PRINSEQ. Note if the input was a PairedEndLibrary, PRINSEQ internally breaks up that object into two separate input files, one for each direction. As a result, more statistical information is generated for PairedEndLibraries. The summary stats can potentially include:

Related Publications

App Specification:

Module Commit: 8d686578cddaee4a9b7b5e3a642cf27f380fc00f