pipeline-resources

About aladdin-shotgun pipeline

This pipeline is designed to conduct taxonomy profiling and diversity analysis on metagenome shotgun sequencing data. Please find the sample report here.

Source of the pipeline

This pipeline is originally adapted from community-developed nf-core/taxprofiler pipeline version 1.0.0. Zymo Research made significant contributions in the adaption effort. This mainly include the addition of downstream analyses such as diversity analysis, addition of sourmash as the profiler, and the improvement of the report.

What is in the pipeline

This pipeline is built using Nextflow. A brief summary of pipeline:

1. Read QC (FastQC or falco as an alternative option)
2. Performs optional read pre-processing
   • Adapter clipping and merging (short-read: fastp, AdapterRemoval2; long-read: porechop)
   • Low complexity and quality filtering (short-read: bbduk, PRINSEQ++; long-read: Filtlong)
3. Perform Host-read removal
   • Host-read removal (short-read: BowTie2; long-read: Minimap2). This is not performed when sourmash-zymo is selected as the database because it already contains host sequences.
   • Statistics for host-read removal (Samtools)
4. Run merging when applicable
5. Performs taxonomic profiling using one of:
   • sourmash
   • MetaPhlAn4
6. Merge all taxonomic profiling results into one table and perform alpha/beta diversity analysis (Qiime2).
7. Compare user samples with already profiled reference datasets (Qiime2)
8. Present all results in above steps in a report (MultiQC)

For details, please find the source code here.