AMPLIPIPER

AMPLIPIPER is a comprehensive yet modular pipeline that is able to perform a wide variety of downstream tasks on raw, basecalled, Oxford Nanopore long reads.

Get started now View it on GitHub

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This website documents the features of the current release (v0.1.0-beta) of AMPLIPIPER. See the CHANGELOG for a list of releases, new features, and bug fixes.

AMPLIPIPER is a pipeline developed by the Naturhistorisches Museum Wien to tackle most of the challenges posed by amplicon sequencing, and its ultimate goal is to provide the user with a comprehensive tool that is able to automatically perform the following tasks in a single run:

• Quality filtering and size selection
• Demultiplexing
• Consensus sequence generation
• Variant calling
• Haplotype calling
• Phylogenetic reconstruction
• Species delimitation
• Species identication

Browse the documentation to learn more about how to use this pipeline!

Quickstart

Here you’ll get a quick tour of the pipeline:

• Installation: To install the pipeline you should have mamba and conda up and running on your machine. Once you are all set, clone the GitHub repository, go inside of it and run:

bash shell/setup.sh

• Installation test: To test that everything is working and get information on the options you can input the pipeline with, run:

bash shell/AmpliPiper.sh -h

• Your first usage: Now that you had a rapid tour of the pipeline’s usage, get ready for the first trial. You should collect the names and the paths of your fastq data in a csv file named samples.csv and the primers (forward and reverse, with their ids, the ploidy of the locus and the expected length of the sequence) in another csv file, named primers.csv. You can then run:

bash /example_absolute_path/AmpliPiper/shell/AmpliPiper.sh \
    -s /example_absolute_path/test/data/samples.csv \
    -p /example_absolute_path/test/data/primers.csv \
    -o /example_absolute_path/test/results/testresults \
    -q 2 \
    -n 500 \
    -t 10 \
    -f \
    -r 250 \
    -m 100 \
    -k 0.08

• Read your results: This previous command will generate all the outputs in the testresults folder: to see a summary of them, run:

firefox /example_absolute_path/test/results/testresults/results.html

See the repository README for a more detailed quickstart.

About the project

Contributors

AMPLIPIPER is developed, distributed and maintained by Martin Kapun (NHM), Sonja Steindl (NHM) and Astra Bertelli (University of Pavia).

Acknowledgments

The present documentation is written with Just the Docs, which is © 2017-2024 Jekyll theme by Patrick Marsceill.

We wish to thank all the amazing people that supported the project and shared advice or opinions about it, as well as all the teams and people behind the software employed in our pipeline.

This project is being developed as part of TETTRIs - Task 6.2, WP6.

License

AMPLIPIPER is an open source project.

Contributing

When contributing to this repository, please first discuss the change you wish to make via issue, email, or any other method with the owners of this repository before making a change.

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