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@lrslab Long Read Sequencing (lrs) lab

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    27 repositories

    • trackcluster-rs

      Public
      sequencingrnaseqpacbio
      sequencingrnaseqpacbiolongreadont
      Rust
      •
      Apache License 2.0
      •0•4•0•0•Updated Apr 26, 2026Apr 26, 2026

    • mtasemotif

      Public
      Python
      •0•1•0•0•Updated Apr 21, 2026Apr 21, 2026

    • CN-AML

      Public
      nanopore whole-genome sequencing of cytogenetically normal acute myeloid leukaemia
      R
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • trackclusterTU

      Public
      Fast interval similarity and scalable clustering for bacterial transcript units (TUs) from mapped long reads.
      rna-seqnanopore-sequencinglongreadsequencing
      rna-seqnanopore-sequencinglongreadsequencing
      Rust
      •
      MIT License
      •1•3•0•0•Updated Apr 8, 2026Apr 8, 2026

    • DVG_ONT_scripts

      Public
      This repository contains a collection of Python and R scripts used for analyzing Nanopore direct RNA sequencing (DRS) data in paper "Unique Production of Abunda…
      R
      •
      Apache License 2.0
      •1•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • benchmark_CycloneSeq

      Public
      The resource table and links to CycloneSeq data processing
      0•0•1•0•Updated Dec 1, 2025Dec 1, 2025

    • Bacteria-Multisequencing

      Public
      Open Repository of Scripts and Resources for Nanopore and NGS Sequencing of Eight Bacteria
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 1, 2025Dec 1, 2025

    • anasfv

      Public
      The analysis pipeline for ASFV genome assembly and phylogenetic analysis.
      Python
      •
      MIT License
      •1•2•1•0•Updated Nov 28, 2025Nov 28, 2025

    • SLRanger

      Public
      Detection tool for operon and spliced leader designed for direct RNA sequencing
      Python
      •0•4•0•0•Updated Nov 5, 2025Nov 5, 2025

    • Hammerhead-motif

      Public
      motif enrichment for hammerhead results
      Python
      •0•0•0•0•Updated Oct 29, 2025Oct 29, 2025

    • CurEA

      Public
      CurEA (Current Event Alignment) Toolkit, designed for CycloneSeq data
      nanopore-sequencing
      nanopore-sequencing
      Rust
      •
      MIT License
      •0•0•0•0•Updated Oct 19, 2025Oct 19, 2025

    • nanoCEM

      Public
      "nanoCEM" is a simple tool designed to visualize the features that distinguish between two groups of ONT data at the site level.
      nanopore-sequencing
      nanopore-sequencing
      Python
      •
      MIT License
      •2•18•1•0•Updated Oct 13, 2025Oct 13, 2025

    • Zebrafish-Multisequencing

      Public
      The scripts used in analyzing the zebrafish datasets.
      Python
      •
      MIT License
      •1•3•0•0•Updated Oct 8, 2025Oct 8, 2025

    • cyclone_plasmid_DNA

      Public
      An example of using Cyclone sequencing to acquire plasmid DNA data for analyzing current changes due to DNA modifications
      Apache License 2.0
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • lrslab.github.io

      Public
      HTML
      •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • nanoSundial

      Public
      A de novo modification detection tool that targets current features based on 004kit for prokaryotes
      nanopore-sequencingrna-modification
      nanopore-sequencingrna-modification
      Python
      •
      Apache License 2.0
      •2•22•0•0•Updated Jul 15, 2025Jul 15, 2025

    • TUFinder

      Public
      An integrated tool for analyzing transcription units (TUs) in prokaryotes using RNA-seq data, with functionalities for identifying transcription start sites (TS…
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 4, 2025Jun 4, 2025

    • Hammerhead

      Public
      This project is designed to find the potential modifications in bacterial genomes.
      Python
      •
      GNU General Public License v2.0
      •1•15•0•0•Updated Nov 6, 2024Nov 6, 2024

    • MethylBin

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • Giraffe_View

      Public
      Giraffe_View is designed to help assess and visualize the accuracy of long-read sequencing datasets.
      nanopore-sequencingquality-benchmarking
      nanopore-sequencingquality-benchmarking
      Python
      •
      MIT License
      •1•13•0•0•Updated Sep 3, 2024Sep 3, 2024

    • DRS_vRNA_modification_content

      Public
      Scripts used in our paper (Utilization of Nanopore Direct RNA Sequencing to analyze intracellular viral RNA modifications of the Sindbis virus)
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 12, 2024Jul 12, 2024

    • ONT_DRS_bacteria_script

      Public
      Script of our Paper "Analysis of Transcriptome and Epitranscriptome in Bacteria Using Nanopore Direct RNA Sequencing"
      Python
      •1•0•0•0•Updated Mar 8, 2024Mar 8, 2024

    • trackclusterv

      Public
      Viral Nanopore direct-RNA sequencing analysis pipeline, designed for RNA virus with complex genomic/subgenomic structures
      Python
      •3•0•0•0•Updated Dec 6, 2023Dec 6, 2023

    • E11assembly

      Public
      The genome assembly annotations for E11 cell line
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Dec 5, 2023Dec 5, 2023

    • Interplay-between-ISVs-and-mosquito-cells-suppl

      Public
      Supplementary figure and tables for our manuscript "Insect-specific chimeric viruses potentiated antiviral responses and curbed pathogenic alphavirus growth in …
      0•0•0•0•Updated Nov 28, 2023Nov 28, 2023

    • Scripts_merge_DRS_methods

      Public
      Scripts to merge tombo and xPore results from ONT data in our Paper (Utilization of Nanopore Direct RNA Sequencing to analyze intracellular viral RNA modificati…
      Python
      •1•0•0•0•Updated Oct 24, 2023Oct 24, 2023

    • Benchmarking_for_ONT_reads

      Public
      The codes used to benchmark ONT reads.
      R
      •
      Apache License 2.0
      •1•4•0•0•Updated May 11, 2023May 11, 2023
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