Frequently Asked Questions

0. I have an issue. How can I report it?

Please open an 'issue' and detail the problem you are having. Please provide information on:

• What section of the pipeline (basecalling, genome assembly, classification, alignment, microbiome analysis, taxonomic classification)
• If you are using a database, which database you are using
• Details on the error message provided
• What you think may have occurred
• If you have tried anything to fix the issue and what you have tried

1. What type of data can I use on this package

To put it simply, nanopore sequenced metagenomic data. Ideally you will use the DNA sequence data although the pipeline also accommodates double-stranded cDNA sequences

2. What type of hardware do I need to run this package

This depends on what you want to do. If you want to run the entire package -- including the basecalling, you will need a GPU and at least a moderately powerful device. However this is not a package to be run on a laptop even one equipped with a GPU. Ideal use of the package should be carried out on a HPC to ensure you have enough memory and processing power to accelerate tasks like genome assembly and compression

3. Do I need to follow your installation instructions to make this work?

Well no, if you are confident in getting the tools and dependencies to work with how you install tools, then that is your prerogative. Some tools here can certainly be installed using other means like pip

4. What is the scope of this package

The package is meant to work for the Sulawesi project it was developed for. However, we hope that it is also adaptable enough for other metagenomic sequence data that fit the requirements described in FAQ 1

5. I'm having issues running the package

Please make sure that you have followed the installation instructions closely. There are a lot of moving parts so it is not unusual that a section may not install as intended. Another thing that may occur is that version changes could break how a tool is expected to work. Hence why we have provided the specific versions we have tested/developed with

6. Will there be a nextflow or containerised version of this?

No. At this point, nextflow/docker and similar systems are not in the works

7. I have got the package installed but I don't know where to start

Please go through the Wiki page and it should give you an in-depth breakdown of how the package works and how to start

8. I have run the package and got results out. What do I do next

Well that's up to you, your resources and research question. After taxonomic classification of the reads and/or the assembly you can carry out a range of subsequent steps. Examples of these include but not limited to functional profiling, polishing/correction, binning, further statistical analyses.

9. I don't have a lot of storage space, and need to delete some outputs. Which ones can I delete?

In most cases, this is up to you however, the biggest storage hogs would be basecalled and demultiplexed reads. After they have been filtered and de-contaminated, both basecalled and demultiplexed output folders can be deleted --with the knowledge that you may need to regenerate them if you want to run the dataset again. Generally the rule is: DO NOT DELETE RAW OR FINAL DATA i.e. do not delete the raw sequence data. If you can easily regenerate the outputs, then you can delete them.

(Updated: 15/12/22. Page in progress. FAQs may be expanded and updated over time)