tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

Collection of tools for the analysis of CpG data

WDL workflows for variant calling and assembly using ONT

VNTR annotation using motif selection

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Basic electric control line model aircraft timer using an Adafruit Trinket M0 & CircuitPython

Workflow management system written as a pure Python package and command-line utility. It supports complex workflows modeled as directed- acyclic graphs (DAGs), and execution on batch schedulers

Pipeline for streamlined fine mapping of potentially causal QTL variants

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF

Comparison of methylation calling between ONT long-read R.9 and R.10 data

Oxford Nanopore's Basecaller

Summarizing the foundational data management, processing, and analysis steps we do in the NIA CARD LRS group.

Tools to parse cramino QC output in bulk and generate an analytics dashboard from the bulk summary.

Firmware for 3 keyboards(QWERTY, GameBoy, Calculator). They are based on MEGA328 chip.

Scripts the CARD long read team uses to query data from the MinKNOW API

Forked CARDlongread-report-parser repository

Scripts and workflows for use analyzing UK Biobank data from the DNANexus Research Analysis Platform

Tools for fiberseq data written in rust.

Source for "The computational guide to Fiber-seq"

scikit-learn: machine learning in Python

Specifications for output files from MinKNOW, dorado and others

An introduction to snakemake on Biowulf

A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules.

QC plots and statistics

Scripts and guidelines for standard benchmarking of methylation calling in Oxford Nanopore (ONT) long read sequencing data

Code repository for analysis performed on NABEC/HBCC ONT WGS data release, including QTL analysis workflows.

Single-cell multiome processing pipeline with downstream analysis modules

Repository for the allele-specifc QTL pipeline developed by the CARD long-read sequencing/applied neurogenomics group.

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads