ONT Shotgun Metagenomics Pipeline -Taxonomic Classification and Genome Assembly

All scripts can be found in bin For the full pipeline documents, please look under docs

This is a repository of scripts and documentation for the analysis of shotgun metagenomic sequencing data generated from Oxford Nanopore Technology (ONT).

This is a relatively new, exciting technology that sequences DNA or RNA by feeding it through a protein nanopore (hole) in a semi-conductor membrane. A major advantage of this technology is it can generate long reads (up to ~23kb) from a single, native molecule (it can be used without PCR if there is a sufficiently large DNA sample). It is also portable, affordable and can sequence in real-time. The main disadvantage is that there is still a relatively high error rate. This project uses a combination of free, third party tools - assuming data base-calling and demultiplexing of the reads has already been completed by the propriety software, ONT-Guppy.

Scripts (in order of pipeline):

1. config.sh
2. data_download.sh
3. longqc.sh
4. fastq_to_fasta
5. classify.sh
6. krona.sh
7. metaflye.sh
8. quast.sh
9. medaka.sh
10. busco.sh

The config.sh file is an optional file that sets the working directory paths to specific variables. Loading it will enable the working directory to be changed easily throughout a working session Please adjust it to suit your file system.