Available Pipelines

SeqDesk ships with built-in support for three bioinformatics pipelines. Each pipeline is a Nextflow workflow designed for a specific analysis type.

MAG (Metagenome-Assembled Genomes)

Pipeline: nf-core/mag v3.4.0 Purpose: Assembly and binning of metagenomes Input: Paired-end FASTQ reads Role required: FACILITY_ADMIN

What MAG Does

The MAG pipeline takes raw metagenomic sequencing reads and produces:

1. Quality-controlled reads — trimmed and host-removed
2. Assembled contigs — via MEGAHIT and/or SPAdes
3. Genome bins — via MetaBAT2, MaxBin2, and/or CONCOCT
4. Refined bins — via DAS Tool
5. Quality scores — completeness and contamination via CheckM
6. Taxonomy — classification via GTDB-Tk
7. QC summary — MultiQC report

Configuration

Outputs

Assemblies and bins are automatically parsed and linked to samples in the database after the run completes.

SubMG (ENA Submission Pipeline)

Pipeline: ttubb/submg Purpose: Automated ENA submission of reads, assemblies, and bins Input: Samples with reads, assemblies, and optionally bins Role required: FACILITY_ADMIN

What SubMG Does

SubMG automates the submission of sequencing data to the European Nucleotide Archive (ENA). It handles the full submission workflow:

1. Validate inputs — checks study/sample prerequisites and ENA credentials
2. Generate config — creates SubMG YAML manifests and helper files
3. Submit — executes submg submit for each manifest
4. Parse receipts — reads ENA responses and stores accession numbers

Prerequisites

Before running SubMG, ensure:

• The study has an ENA study accession (PRJEB...)
• Samples have taxonomy IDs assigned
• Reads are linked to samples
• ENA credentials are configured (see ENA Credentials)

Configuration

Outputs

After a successful run, accession numbers are stored back in the database:

• Sample accessions — ERS/SAMEA numbers
• Read accessions — ERX/ERR numbers
• Assembly accessions — linked to Assembly records
• Bin accessions — linked to Bin records

MetaxPath (Pathogen Profiling)

Pipeline: hzi-bifo/MetaxPath v0.1.0 Purpose: Long-read clinical metagenomics for pathogen identification, virulence, and AMR detection Input: Long-read FASTQ files (Oxford Nanopore or PacBio) Role required: FACILITY_ADMIN

What MetaxPath Does

MetaxPath is designed for clinical metagenomics on long-read sequencing data. It performs:

1. Human-read filtering — removes host contamination
2. Taxonomic profiling — via Metax and Sylph
3. Assembly — via Flye (or configurable assemblers)
4. Virulence factor prediction — identifies pathogenic gene markers
5. AMR detection — predicts antibiotic resistance genes
6. Reporting — generates HTML reports and species abundance dotplots

Supported Sequencers

• Oxford Nanopore (MinION, GridION, PromethION)
• PacBio (Sequel, Revio)

Configuration

Database paths (must be configured by admin):

Outputs

Adding More Pipelines

SeqDesk supports adding custom pipelines through a package structure. See Adding Custom Pipelines for details on creating your own pipeline integrations.