PEPPER
is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline. This pipeline enables nanopore-based variant calling with DeepVariant.
Please cite the following manuscript if you are using PEPPER-Margin-DeepVariant
:
In a project led by Professor Euan Ashley, the team demonstrated the ability to identify clinically actionable disease causing variants in a critical care setting with nanopore sequencing and PEPPER-Margin-DeepVariant
.
Following are the publications that demonstrate the performance of PEPPER-Margin-DeepVariant
in a clinical setup:
Clinical report:
Case report:
Detailed variant calling performance evaluation:
Please follow the case-studies documentation for PacBio-HiFi and ONT 10.4 Q20 performance evaluation.
PEPPER-Margin-DeepVariant can be run using Docker or Singularity. A simple docker command looks like:
sudo docker run \
-v "${INPUT_DIR}":"${INPUT_DIR}" \
-v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \
kishwars/pepper_deepvariant:r0.8 \
run_pepper_margin_deepvariant call_variant \
-b "${INPUT_DIR}/${BAM}" \
-f "${INPUT_DIR}/${REF}" \
-o "${OUTPUT_DIR}" \
-t "${THREADS}" \
--ont_r9_guppy5_sup
# --ont_r9_guppy5_sup is preset for ONT R9.4.1 Guppy 5 "Sup" basecaller
# for ONT R10.4 Q20 reads: --ont_r10_q20
# for PacBio-HiFi reads: --hifi
Test type | Links |
---|---|
Docker quickstart | Link |
Singularity quickstart | Link |
Docker-gpu quickstart | Link |
Pipeline | Docker | Singularity | NVIDIA-docker (GPU) |
---|---|---|---|
Nanopore R9.4.1 variant calling |
Link | Link | Link |
Nanopore R10.4 Q20 variant calling |
Link | Link | Link |
PacBio HiFi variant calling |
Link | Link | Link |
PEPPER license, Margin License and DeepVariant License extend to the trained models (PEPPER, Margin and DeepVariant) and container environment (Docker and Singularity).
We are thankful to the developers of these packages:
PEPPER-Margin-DeepVariant pipeline is developed in a collaboration between UC Santa Cruz genomics institute and the Genomics team in Google Health.
The name "P.E.P.P.E.R." is inspired from an A.I. created by Tony Stark in the Marvel Comics (Earth-616).
PEPPER is named after Tony Stark's then friend and the CEO of Resilient, Pepper Potts.