illumiprocessor: parallel adapter and quality trimming

Release v2.0. (Changelog)

illumiprocessor is a tool to batch process illumina sequencing reads using the excellent trimmomatic package. The program takes as input the location of your demultiplexed illumina reads, a configuration file that is formatted in Microsoft Windows INI file format (key:value pairs, see the example file), and the output directory in which you want to store the trimmed reads.

illumiprocessor will trim adapter contamination and low quality bases from SE and PE illumina reads, and the program is also capable of dealing with double-indexed reads . The current version of illumiprocessor uses trimmomatic instead of scythe and sickle (used in v1.x) because we have found the performance of trimmomatic to be better, particularly when dealing with double-indexed illumina reads. However, you may find that running scythe after trimming with illumiprocessor may ensure that every bit of potential adapter contamination is removed.

illumiprocessor is suited to parallel processing in which each set of illumina reads are processed on a separate (physical) compute core. illumiprocessor assumes that all fastq files input to the program represent individuals samples (i.e., that you have merged mulitple files for each read from the same sample by combining fastq.gz files).