- Guppy v4.2.2 (Commercial software from Oxford Nanopore Technologies)
- Minimap2 v2.17-r974
- PEPPER v0.5 (Docker image -
kishwars/pepper_deepvariant:test-v0.5) - Margin (Docker image -
kishwars/pepper_deepvariant:test-v0.5) - Google DeepVariant
- none model (Docker image -
kishwars/pepper_deepvariant:test-v0.5) - rows model (Docker image -
kishwars/pepper_deepvariant:test-v0.5-rows)
- none model (Docker image -
- Utilities: docker, samtools v1.11, bgzip v1.11, tabix v1.11, GNU parallel
- Sniffles v1.0.12
- SV Annotation (Docker image -
quay.io/jmonlong/svnicu:0.5)
Our pipeline was set up on the Google Cloud Platform but can easily be ported to other cloud platforms using similar configuration of instances as above.
- Install Google Cloud SDK (Instructions for a non-GCP instance)
- Login with the Google Cloud Platform account account
gcloud auth login
You will be redirected to a webpage/provided a link for the google login with the above account.
- To check the current settings/project in use
gcloud init
Set up the custom instance images and templates based on these instructions.
There is 1 demo test set provided for each stage -- guppy-minimap2, PEPPER-Margin-DeepVariant, Sniffles, Annotation. Every demo requires a host instance, the instructions for which are provided here
Please cite the following manuscript if you are using the pipeline:
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing (Nature Biotechnology)
Authors: Sneha D. Goenka, John E. Gorzynski, Kishwar Shafin, Dianna G. Fisk, Trevor Pesout, Tanner D. Jensen, Jean Monlong, Pi-Chuan Chang, Gunjan Baid, Jonathan A. Bernstein, Jeffrey W. Christle, Karen P. Dalton, Daniel R Garalde, Megan E. Grove, Joseph Guillory, Alexey Kolesnikov, Maria Nattestad, Maura R.Z. Ruzhnikov, Mehrzad Samadi, Ankit Sethia, Elizabeth Spiteri, Christopher J. Wright, Katherine Xiong, Tong Zhu, Miten Jain, Fritz J. Sedlazeck, Andrew Carroll, Benedict Paten, and Euan A. Ashley