novoalab Goto Github PK
Name: Novoa Lab
Type: Organization
Bio: Epitranscriptomics and RNA Dynamics Laboratory @CRG (Barcelona, Spain)
Twitter: NovoaLab
Location: Spain
Name: Novoa Lab
Type: Organization
Bio: Epitranscriptomics and RNA Dynamics Laboratory @CRG (Barcelona, Spain)
Twitter: NovoaLab
Location: Spain
Benchmarked base calling models for nanopore sequencing providing super high accuracy and improved RNA modification detection
Best practices for the Analysis of Oxford Nanopore Direct RNA sequencing Data (Begik*, Lucas*, et al., bioRxiv 2020)
Compute codon autocorrelation from fasta CDS sequences (Novoa et al., Mol Biol Evol 2019)
Signal based nanopore RNA demultiplexing with convolutional neural networks (Smith*, Ersavas*, Ferguson* et al., Genome Research 2020)
Tools to process and analyze deep sequencing data.
Scripts for identifying sites with differential error rates in mapped nanopore DRS data
Direct RNA sequencing (DRS) analysis included in article: N6-methyladenosine modification is not a general trait of viral RNA genomes
Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
Website for NovoaLab, built by the NovoaLab team
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 for Github Readme.md
Nextflow pipeline for analysis of direct RNA Nanopore reads (Cozzuto et al., Front in Genet 2020)
modPhred is a pipeline for detection of DNA/RNA modifications from raw ONT data
From samtools mpileup to stats of coverage, ref_nuc, mismatches, deletions, insertions, RT-stops
Quantitative analysis of native tRNA populations using direct RNA nanopore sequencing (Lucas*, Pryszcz* et al., Nat Biotech 2023)
Nanopore 3' end-capture sequencing (Begik et al., bioRxiv 2021)
Prediction of RNA modifications and their stoichiometry from per-read features: current intensity, dwell time and trace (Begik*, Lucas* et al., Nature Biotech 2021)
Detection of Nm sites from Nanopore DRS data
Pipeline for Ribosome Profiling Data
Analyses from manuscript: Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures (Begik et al. Genome Biology 2020).
Scripts used to produce plots in the RPL3L manuscript
SquiggleKit: A toolkit for manipulating nanopore signal data
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
original hoffmann pipeline, with changes for portability
UNC-Chapel Hill Bioinformatics Utilities
Analysis of Direct RNA Sequencing of Yeast Ribosomal RNA
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