Name: Hasindu Gamaarachchi
Type: User
Company: UNSW Sydney and Garvan Institute of Medical Research
Bio: I am currently working on domain-specific computer systems for ultra-efficient real-time genomic data processing
Twitter: Hasindu2008
Location: Australia
Blog: https://www.linkedin.com/in/hasindugamaarachchi/
Hasindu Gamaarachchi's Projects
C/C++ implementation of ARTIC bioinformatics platform for nanopore sequencing of nCoV2019 novel coronavirus
A curated list of awesome nanopore analysis tools.
Conda recipes for the bioconda channel.
My random bioinformatics tools
The buttery eel - a slow5 guppy basecaller wrapper
Burrow-Wheeler Aligner for short-read alignment on arm based devices (see minimap2 for long-read alignment)
Spurious alignment Removal, distributed splitting and data transfer for swaram
Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)
Lightweight job scheduler and daemon for nanopore data processing on a mini-cluster
De novo assembler for single molecule sequencing reads using repeat graphs
Miscellaneous helpers
C library for high-throughput sequencing data formats - patched for FASTT index
Adaptive Banded Event Alignment
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Data and analysis for NA12878 genome on nanopore
Signal-level algorithms for MinION data
Lossless compression for nanopore DNA signal data
PBS scripts for running nanopore genomics analyses on NCI Gadi
GPU-accelerated Dynamic Time Warp (DTW) Barycenter Averaging
Cache Optimised Platypus Variant Caller
The A to Z of Building a Testbed for Power Analysis Attacks
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)
Complements Minimap2 for a fast and efficient Read-Until pipeline
R wrapper for slow5lib
Support scripts for SWARAM