← Sequencing & variant calling

PEPPER-Margin-DeepVariant

Haplotype-aware variant calling pipeline for nanopore reads combining PEPPER, Margin and DeepVariant.

Visit website ↗

CategorySequencing & variant calling
GitHubkishwarshafin/pepper
First public2020-10-09 (source)
Paperhttps://doi.org/10.1038/s41592-021-01299-w
LicenseMIT
PricingOpen source
Tags#variant-calling#nanopore#phasing
Last checked2026-10-16

Specs

Sequencing platformOxford Nanopore
TaskHaplotype-aware variant calling, polishing
Variant types—
GitHub stars261
InterfaceDocker

Specs come from each project's README, paper or official page · PEPPER-Margin-DeepVariant README · PEPPER-Margin-DeepVariant paper. “—” means we couldn't verify it.

Compare with…

Pick 1–3 other Sequencing & variant calling tools to compare side by side with PEPPER-Margin-DeepVariant.

Select 1–3 tools

Related

DeepVariant

Google deep learning variant caller for Illumina, PacBio HiFi and ONT data.

Sequencing & variant callingOpen source#variant-calling#long-read

Dorado

Oxford Nanopore's production basecaller: transformer/LSTM models turning raw nanopore signal into reads, with modified-base calling and duplex.

Sequencing & variant callingOpen source#basecalling#nanopore

Bonito

Oxford Nanopore's research basecaller for training and testing new basecalling models.

Sequencing & variant callingOpen source#basecalling#nanopore