hasindu2008
I am currently working on domain-specific computer systems for ultra-efficient real-time genomic data processing
UNSW Sydney and Garvan Institute of Medical ResearchAustralia
Pinned Repositories
f5c
Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)
f5p
Lightweight job scheduler and daemon for nanopore data processing on a mini-cluster
libabea
Adaptive Banded Event Alignment
minimap2-arm
A versatile pairwise aligner for genomic and spliced nucleotide sequences
nci-scripts
PBS scripts for running nanopore genomics analyses on NCI Gadi
sigfish
Align raw nanopore signals to a reference using subsequence DTW
sigtk
A simple toolkit for manipulating nanopore signal data
slow5lib
slow5lib is a software library for reading & writing SLOW5 files.
slow5tools
Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.
squigulator
a tool for simulating nanopore raw signal data
hasindu2008's Repositories
hasindu2008/f5c
Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)
hasindu2008/slow5tools
Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.
hasindu2008/squigulator
a tool for simulating nanopore raw signal data
hasindu2008/slow5lib
slow5lib is a software library for reading & writing SLOW5 files.
hasindu2008/sigtk
A simple toolkit for manipulating nanopore signal data
hasindu2008/sigfish
Align raw nanopore signals to a reference using subsequence DTW
hasindu2008/nci-scripts
PBS scripts for running nanopore genomics analyses on NCI Gadi
hasindu2008/seq
Publicly available nanopore datasets (with raw data)
hasindu2008/RawHash
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)
hasindu2008/slow5specs
Specification of the SLOW5 file format
hasindu2008/rslow5
R wrapper for slow5lib
hasindu2008/slowION
a benchmark tool that can simulate data rates of a nanopore sequencer
hasindu2008/hlib
Miscellaneous helpers
hasindu2008/slorado
A simplified version of Dorado built on top of S/BLOW5 format.
hasindu2008/slow5
SLOW5 Ecosystem Website
hasindu2008/awesome-nanopore
A curated list of awesome nanopore analysis tools.
hasindu2008/bioconda-recipes
Conda recipes for the bioconda channel.
hasindu2008/biorand
My random bioinformatics tools
hasindu2008/buttery-eel
The buttery eel - a slow5 guppy basecaller wrapper
hasindu2008/hasindu2008.github.io
hasindu2008/nanopolish-arm
Signal-level algorithms for MinION data
hasindu2008/nanopress
Lossless compression for nanopore DNA signal data
hasindu2008/OpenDBA
GPU-accelerated Dynamic Time Warp (DTW) Barycenter Averaging
hasindu2008/Optimised-Read-Until-API
hasindu2008/RawMap
Complements Minimap2 for a fast and efficient Read-Until pipeline
hasindu2008/sg-nex-data
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
hasindu2008/sigmap
A streaming method for mapping nanopore raw signals
hasindu2008/slow5-template
A template repository that demonstrates how slow5lib can be used to develop a new nanopore tool
hasindu2008/slow5-template-x
A template that demonstrates the advanced use of slow5lib
hasindu2008/SquiggleKit
SquiggleKit: A toolkit for manipulating nanopore signal data