Novoa Lab

EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)

nanoRMS

Prediction of RNA modifications and their stoichiometry from per-read features: current intensity, dwell time and trace (Begik*, Lucas* et al., Nature Biotech 2021)

modPhred

modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data

m6ABasecaller

An m6A-aware basecalling model to detect m6A modifications at single nucleotide resolution in individual reads (Cruciani, Delgado-Tejedor, Pryszcz et al., BioRxiv 2023)

Nano-tRNAseq

Quantitative analysis of native tRNA populations using direct RNA nanopore sequencing (Lucas*, Pryszcz* et al., Nat Biotech 2023)

Nano3P_Seq

Nanopore 3' end-capture sequencing (Begik et al., bioRxiv 2021)

Best_Practices_dRNAseq_analysis

Best practices for the Analysis of Oxford Nanopore Direct RNA sequencing Data (Begik*, Lucas*, et al., bioRxiv 2020)

basecalling_models

Benchmarked base calling models for nanopore sequencing providing super high accuracy and improved RNA modification detection

yeast_RNA_Mod

Analysis of Direct RNA Sequencing of Yeast Ribosomal RNA

codonAutocorrelation

Compute codon autocorrelation from fasta CDS sequences (Novoa et al., Mol Biol Evol 2019)

RNAModMachinery

Analyses from manuscript: Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures (Begik et al. Genome Biology 2020).

differr_nanopore_DRS

Scripts for identifying sites with differential error rates in mapped nanopore DRS data

SquiggleKit

SquiggleKit: A toolkit for manipulating nanopore signal data

ubu

UNC-Chapel Hill Bioinformatics Utilities

DeePlexiCon

Signal based nanopore RNA demultiplexing with convolutional neural networks (Smith*, Ersavas*, Ferguson* et al., Genome Research 2020)

MasterOfPores

Nextflow pipeline for analysis of direct RNA Nanopore reads (Cozzuto et al., Front in Genet 2020)

RPL3L

Scripts used to produce plots in the RPL3L manuscript

deepTools

Tools to process and analyze deep sequencing data.

DRS_CHIKV_Analysis

Direct RNA sequencing (DRS) analysis included in article: N6-methyladenosine modification is not a general trait of viral RNA genomes

lab_website

Website for NovoaLab, built by the NovoaLab team

markdown-cheatsheet

Markdown Cheatsheet for Github Readme.md

mpileup2stats

From samtools mpileup to stats of coverage, ref_nuc, mismatches, deletions, insertions, RT-stops

Nm_Nanopore_Drosophila

Detection of Nm sites from Nanopore DRS data

novoalab.github.io

riboflow

Pipeline for Ribosome Profiling Data

tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

tRNAmap_Hoffmann_adapted

original hoffmann pipeline, with changes for portability