illumiprocessor is a tool to batch process illumina sequencing reads using the excellent trimmomatic package. The program takes a configuration file that is formatted in Microsoft Windows INI file format (key:value pairs, see the example file).
illumiprocessor will trim adapter contamination from SE and PE illumina reads and is capable of dealing with double-indexed reads and read trimming (example to come shortly). 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 or trimmomatic ensures 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).
- HPC_ILLUMIPROCESSOR_DIR - installation directory
If you publish research that uses illumiprocessor you have to cite it as follows:
Faircloth, BC. 2013. illumiprocessor: a trimmomatic wrapper for parallel adapter and quality trimming. http://dx.doi.org/10.6079/J9ILL.
Please be sure also to cite trimmomatic:
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics. http://dx.doi.org/10.1093/bioinformatics/btu170.