The MG-RAST pipeline incorporates a series of steps for quality control and artifacts removal, ensuring robust processing of metagenomic and metatranscriptome datasets. The initial stage involves trimming low-quality regions using SolexaQA and eliminating reads with inappropriate lengths. In the case of metagenome and metatranscriptome datasets, a dereplication step is introduced to enhance data processing efficiency.
The subsequent step employs DRISEE (Duplicate Read Inferred Sequencing Error Estimation) to evaluate sample sequencing errors by measuring Artificial Duplicate Reads (ADRs). This assessment contributes to enhancing the accuracy of downstream analyses.
Finally, the pipeline offers the option to screen reads using the Bowtie aligner. It identifies and removes reads that exhibit matches close to the genomes of model organisms, including fly, mouse, cow, and human. This step aids in refining the dataset by filtering out reads associated with potential contaminants or unintended sequences.