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.
config.shdata_download.shlongqc.shfastq_to_fastaclassify.shkrona.shmetaflye.shquast.shmedaka.shbusco.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.