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basecalling_models

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

best_practices_drnaseq_analysis

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

codonautocorrelation

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

deeplexicon

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

deeptools

Tools to process and analyze deep sequencing data.

differr_nanopore_drs

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

drs_chikv_analysis

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

epinano

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

lab_website

Website for NovoaLab, built by the NovoaLab team

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)

markdown-cheatsheet

Markdown Cheatsheet for Github Readme.md

masterofpores

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

modphred

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

mpileup2stats

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

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)

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)

nm_nanopore_drosophila

Detection of Nm sites from Nanopore DRS data

novoalab.github.io

riboflow

Pipeline for Ribosome Profiling Data

rnamodmachinery

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

rpl3l

Scripts used to produce plots in the RPL3L manuscript

squigglekit

SquiggleKit: A toolkit for manipulating nanopore signal 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

ubu

UNC-Chapel Hill Bioinformatics Utilities

yeast_rna_mod

Analysis of Direct RNA Sequencing of Yeast Ribosomal RNA