chloroscan 0.1.0

A computational workflow designed to recover plastid genomes from metagenomes.

Author: Yuhao Tong (The University of Melbourne)

A snakemake workflow for MMA metagenomics for recovering chloroplast genomes.

Project implementation commence date: August 8th, 2023 This workflow will try to cover all essential steps in order to get down the genomics-based metagenomic analysis in recovering algal plastidial genomes. Before starting the new jobs:

1. Set-up the binny workflow within ChloroScan working directory.

2. Set-up the CAT-taxonomy identification database, for details please see this: https://tbb.bio.uu.nl/bastiaan/CAT_prepare/

3. Make sure the FragGeneScanRs is added to your path.

All steps above have been covered by running autoInit.sh.

Modules of the workflow:

1. bio-corgi: Contig classification to filter out plastid contigs.

2. binny (Customized for ChloroScan): cluster contigs into bins/Metagenome-Assembled genomes (MAGs).

3. CAT/BAT: the taxonomy assignment of each contig to help identifying the taxon of bins (this workflow uses conda version of CAT/BAT, meanwhile the nr database has been updated to 2023/11/20).

4. summary.py: The tabular storing of binning and taxonomic identification info that can augment further interpretation of the data.

5. visualization.py: using the spreadsheet output from summary.py, visualize contig clustering info via scatterplot, taxonomy via pie chart and contig depth violin plot.

6. refinement.py: remove contigs within bins that are “not taxonomically identified as eukaryotic” AND contains no markers predicted from database used by binny.

7. CDS extraction: FragGeneScanRs (installed via cargo) predicts ORF from contigs and gffread will turn gff files into fasta format to enable downstream analysis.

8. Dataset microbial community visualization: via Krona, that produces a pie chart to visualize microbial taxonomic groups in metagenome.

Currently ChloroScan is only available via from-resource installation.

Once the workflow gets finished, the recovered MAGs will be passed to the snakemake workflow Orthoflow (https://rbturnbull.github.io/orthoflow/main/installation.html), to conduct the phylogenetic analysis and see if there any new insights brought by these MAGs.

To install ChloroScan from resource:

git clone https://github.com/Andyargueasae/chloroscan.git
cd chloroscan
poetry install
poetry shell

Future Update:

1. Comprehensive algae lineage-specific marker gene database (in development).

For detailed information for installation, fine-tuning workflow and instruction of configuration of ChloroScan, please don’t hesitate to visit the wiki website for details: https://andyargueasae.github.io/chloroscan/. And for further discussion of your bugs and difficulties in running ChloroScan, visit issues.