Metagenomics

This metagenomics pipeline processes raw or aligned sequencing data (BAM or FASTQ)—to quantify species abundance across barcoded samples. It is optimized for evaluating pathogen detection sensitivity and contamination in dilution series experiments. The workflow is compatible with custom reference FASTA files.

Key Features:

• Accepts BAM or FASTQ input per barcode

• Reference-based mapping with automatic index generation

• Alignment filtering by orientation and mapped read status

• Customizable accession-to-species mapping

Outputs:

• Per-barcode aligned files of mapped reads

• Final summary table including:

  • Barcode

  • Species

  • Aligned Read Count

  • Aligned Base Count

This pipeline is ideal for:

• Microbial community profiling

• Pathogen dilution series or detection limit testing

• Contamination tracking across multiplexed samples

• Clinical or research-based metagenomics workflows