Reaper

Reaper processes short read sequencing data to demultiplex reads by barcode, trim adapter sequences and low-quality bases, and filter artifacts to prepare datasets for downstream genomic, transcriptomic, and metagenomic analyses.

Key Features:

• Demultiplexing: Segregates mixed sequencing reads into samples based on barcode sequences.
• Trimming: Removes adapter sequences and trims low-quality bases from reads.
• Filtering: Applies stringent criteria to remove sequencing artifacts and erroneous reads.
• EMBL-EBI integration: Interoperates with EMBL-EBI resources, explicitly including the European Variation Archive and EMPIAR.

Scientific Applications:

• Genomics: Prepares high-quality short read datasets for identification of genetic variation and variant analysis.
• Transcriptomics: Produces cleaned reads suitable for gene expression quantification and transcriptome profiling.
• Metagenomics: Generates filtered reads for characterization of microbial community composition and diversity.

Methodology:

Uses advanced algorithms to perform barcode-based demultiplexing, adapter and base-quality trimming, and stringent read filtering, and integrates with the European Variation Archive and EMPIAR for interoperability with public repositories.