Hasindu Gamaarachchi
hasindu2008
I am currently working on domain-specific computer systems for ultra-efficient real-time genomic data processing
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Top Repositories
Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)
Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.
a tool for simulating nanopore raw signal data
slow5lib is a software library for reading & writing SLOW5 files.
adaptive genome assembly using nanopore sequencing
A simple toolkit for manipulating nanopore signal data
Repositories
53adaptive genome assembly using nanopore sequencing
a tool for simulating nanopore raw signal data
Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.
User-friendly interface for GPGPU programming. Allows running CUDA applications through a web interface rather than from a traditional command line.
slow5lib is a software library for reading & writing SLOW5 files.
A simple toolkit for manipulating nanopore signal data
Conda recipes for the bioconda channel.
Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)
PBS scripts for running nanopore genomics analyses on NCI Gadi
SLOW5 Ecosystem Website
a benchmark tool that can simulate data rates of a nanopore sequencer
Benchmarking SLOW5 vs POD5
My random bioinformatics tools
Align raw nanopore signals to a reference using subsequence DTW
product details
No description provided.
Publicly available nanopore datasets (with raw data)
Lightweight job scheduler and daemon for nanopore data processing on a mini-cluster
RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)
The A to Z of Building a Testbed for Power Analysis Attacks
The buttery eel - a slow5 guppy basecaller wrapper
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Lossless compression for nanopore DNA signal data
A simplified version of Dorado built on top of S/BLOW5 format.
R wrapper for slow5lib
Cache Optimised Platypus Variant Caller
Burrow-Wheeler Aligner for short-read alignment on arm based devices (see minimap2 for long-read alignment)
A simple BAM file parser
C library for high-throughput sequencing data formats - patched for FASTT index
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project