CycScan (Cycle Scan)

CycScan is a pipeline to investigate elemental cycles in metagenomic assemblies or metagenome-assembled genomes (MAGs).

• Before running: Please make sure CycScan_DB.dmnd CycScan_DB_anno.txt elemental_cycle_pathways.tsv are available in dir CycScan_DB before run this pipeline. If not, pls prepare these files using provided scripts.

Installation

Step 1. Create a conda environment

conda create -n cycscan -y
conda activate cycscan

#mamba is recommend
mamba install wget parafly diamond=2.0.15 prodigal=2.6.3 coverm -y 
#or
#conda install wget parafly diamond=2.0.15 prodigal=2.6.3 coverm -y

Step 2. Download or clone CycScan repository

git clone https://github.com/jchenek/CycScan.git

Step 3. Prepare database (run this step in dir 'CycScan_DB')

#run following scripts one by one, pay attention to the std output info of each script
sh DB_prep_s1_get_ko_genes.sh
perl DB_prep_s2_get_gene_seqs.pl ko_genes.txt
sh DB_prep_s3_make_DB_and_sapce_release.sh

Usage

• Step 1: Cycles identification

You may check cycle maps in dir 'Cycle_MAPs'.

conda activate cycscan
perl /PATH/TO/Cyciden.pl -i /PATH/TO/YOUR/fa_dir -p /PATH/TO/CycScan_dir