Hasindu Gamaarachchi

Open-source, Hardware-Independent GPU Acceleration for Scalable Nanopore Basecalling with Slorado and Openfish

This paper introduces open-source GPU-accelerated basecalling tools for nanopore sequencing that are hardware-independent and competitive with proprietary solutions.

Integrative genomics of the siphonophore Physalia utriculus reveals the regulatory logic of colonial division of labour and the molecular basis of venom activity

This study presents a multi-omic atlas of the siphonophore Physalia utriculus, revealing the regulatory mechanisms of colonial division of labour and the molecular basis of venom activity.

Panomap: Unbiased Nanopore Signal Mapping with Pangenome Variation Graphs

Panomap maps raw nanopore signals to pangenome variation graphs, improving mapping accuracy and reducing reference bias compared to linear-reference methods.

DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage

The paper examines DNA methylation dynamics in marsupial embryos, finding global demethylation in the trophectoderm but not the embryonic lineage, suggesting 5mC erasure in extraembryonic tissue is ancestral in therian mammals.

Targeted sequencing and iterative assembly of near-complete genomes

The paper introduces Cornetto, a method using targeted long-read sequencing to improve genome assembly quality and completeness, particularly for challenging regions and sample types.

Base modification analysis in long read sequencing data using Minimod

This paper introduces minimod, a tool for analyzing base modifications in long-read sequencing data, showing significant speed improvements over existing tools.

A new compression strategy to reduce the size of nanopore sequencing data

This paper introduces ex-zd, a compression strategy for nanopore sequencing data that reduces file sizes by removing redundant bits without affecting downstream analyses.

Realfreq: Real-time base modification analysis for nanopore sequencing

Realfreq provides real-time base modification analysis for nanopore sequencing, enabling live data analysis during sequencing.

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

This study benchmarks Nanopore long read RNA sequencing in human cell lines, showing improved isoform resolution compared to short reads.

Targeted long-read sequencing as a single assay improves diagnosis of spastic-ataxia disorders

This paper demonstrates that targeted long-read sequencing improves genetic diagnosis of spastic-ataxia disorders by identifying causative variants in 41% of undiagnosed cases using a single assay.

The enduring advantages of the SLOW5 file format for raw nanopore sequencing data

This paper compares POD5 and SLOW5 file formats for nanopore sequencing data, finding SLOW5 offers better performance, lower cost, and easier management.

Leveraging Basecaller's Move Table to Generate a Lightweight k-mer Model

This paper develops a lightweight k-mer model for RNA004 chemistry using basecaller move tables, achieving high alignment rates and comparable m6A detection performance to default models.

Squigulator: simulation of nanopore sequencing signal data with tunable noise parameters

Squigulator simulates nanopore sequencing signals with tunable noise parameters to test and improve analysis methods.

Extensive DNA methylome rearrangement during early lamprey embryogenesis

This study investigates DNA methylation dynamics during lamprey embryogenesis, revealing extensive maternal-to-paternal epigenome remodeling and its link to programmed genome rearrangement.

Interactive visualisation of raw nanopore signal data with Squigualiser

Squigualiser provides an interactive visualization tool for nanopore signal data, enabling alignment to reference genomes and comparison of multiple datasets.

Streamlining remote nanopore data access with slow5curl

slow5curl enables efficient retrieval of specific nanopore reads from large datasets, reducing storage and transfer costs for reanalysis.

The landscape of genomic structural variation in Indigenous Australians

This study profiles genomic structural variation in Indigenous Australians using whole genome long-read sequencing, revealing abundant and previously unannotated variants and unique STR diversity.

minimap2-fpga: Integrating hardware-accelerated chaining for efficient end-to-end long-read sequence mapping

The paper introduces minimap2-fpga, a hardware-accelerated version of minimap2 that improves mapping speed for long-read sequencing data with minimal accuracy loss.

Accelerated nanopore basecalling with SLOW5 data format

This paper introduces Buttery-eel, an open-source tool that accelerates nanopore basecalling by leveraging the SLOW5 data format for efficient data access on HPC and cloud environments.

Flexible and efficient handling of nanopore sequencing signal data with slow5tools

slow5tools converts and manipulates nanopore sequencing data in the SLOW5 format, offering efficient and flexible data handling with performance improvements over FAST5.

DeepSelectNet: Deep Neural Network Based Selective Sequencing for Oxford Nanopore Sequencing

DeepSelectNet improves selective sequencing accuracy for species classification, outperforming existing methods and enabling real-time classification.

Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing

This study develops a programmable nanopore sequencing assay for diagnosing all known pathogenic STRs in a single test, accurately diagnosing 27 patients with neurogenetic disorders.

InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses

InterARTIC provides a web tool for analyzing whole-genome nanopore sequencing data of viruses, enabling users to reconstruct consensus sequences without bioinformatics expertise.

SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis

The paper introduces SLOW5, a new file format for nanopore sequencing data that accelerates analysis on HPC systems by enabling efficient parallelization.

Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

This study evaluates the analytical validity of nanopore sequencing for SARS-CoV-2 genome analysis, finding high accuracy for SNVs but limitations in detecting short indels and low-frequency variants.

GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative Nanopore Signal Analysis

This paper introduces f5c, a GPU-optimized implementation of Adaptive Banded Event Alignment for faster nanopore signal analysis and DNA methylation detection.

F5N : Nanopore Sequence Analysis Toolkit for Android Smartphones

F5N enables nanopore sequence analysis on Android smartphones using existing tools, completing methylation calling in 15 minutes for 4000 reads.

Featherweight long read alignment using partitioned reference indexes

The paper reduces memory requirements for long read alignment on mobile devices by optimizing parameters and merging techniques, enabling human genome alignment with 2GB RAM without accuracy loss.