Assembleflow

Assembleflow is a metagenomic sequencing assembly pipeline for Illumina paired-end reads. It assembles reads into contigs and assigns a taxonomic rank to each contig. The pipeline is implemented in Nextflow and is designed for high-throughput analysis.

Requirements

• Conda
• Nextflow

Installation

Before running Assembleflow, you need to build a DIAMOND database for taxonomic assignment. You can do this by running the following script:

bash build_diamond_db.sh

Note: The DIAMOND database requires hundreds of gigabytes of disk space. Make sure you have sufficient storage before proceeding.

Pipeline Overview

Assembleflow consists of the following steps:

1. Preprocessing Reads

   • Merging overlapping read pairs
   • Adapter trimming

2. Assembly

   • Assemble reads into contigs
   • Align reads back to contigs
   • Detect circular contigs

3. Taxonomic Assignment

   • Assign taxonomy using DIAMOND
   • Retrieve taxonomic lineage information

Configuration & Usage

You need to update the nextflow.config file before running Assembleflow.

Key Parameters

Parameter	Description	Example
reads	Folder containing paired-end sequence reads	./test/*{R1,R2}.fastq.gz
adapt	File containing adapter sequences (FASTA format)	./bin/adapter_sequences.fasta
db	Path to the DIAMOND database	./refseq_protein_db/refseq_protein_diamond.dmnd
outdir	Output directory for results	./test/results/

Running the Pipeline

Once your nextflow.config file is properly set up, run the pipeline with:

nextflow run main.nf