Method to filter Illumina sequence data by removing low quality reads and reads mapping to artifact and contamination databases using BBTools. DNA sequencing produces low quality reads, reads that contain sequencing artifacts and contamination from lab processes. Removing the bad data from the fastq produces more accurate results for mapping to references and assembly. BBTools is a bioinformatics software package developed at the DOE Joint Genome Institute and used worldwide. http://bbtools.jgi.doe.gov