Pinned Repositories
snap
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
abPOA
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
academicpages.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
al-folio
A beautiful Jekyll theme for academics
Assembly-methods-nanopore
Assembly methods for nanopore-based metagenomic sequencing: a comparative study
aws-fpga-app-notes
Application notes for the F1 EC2 Instance
bwa-mem2
Building upon BWA-MEM2, this repository includes performance improvements to the seeding and mate-rescue steps.
genomicsbench
A benchmark suite to study the performance characteristics of genomics applications
snap
Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
bwa-mem2
The next version of bwa-mem
arun-sub's Repositories
arun-sub/genomicsbench
A benchmark suite to study the performance characteristics of genomics applications
arun-sub/bwa-mem2
Building upon BWA-MEM2, this repository includes performance improvements to the seeding and mate-rescue steps.
arun-sub/abPOA
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
arun-sub/academicpages.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
arun-sub/Assembly-methods-nanopore
Assembly methods for nanopore-based metagenomic sequencing: a comparative study
arun-sub/basejump_stl
BaseJump STL: A Standard Template Library for SystemVerilog
arun-sub/bonito
Convolutional Basecaller for Oxford Nanopore Reads
arun-sub/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
arun-sub/canu
A single molecule sequence assembler for genomes large and small.
arun-sub/deBruijn
arun-sub/fastmac
arun-sub/Flye
De novo assembler for single molecule sequencing reads using repeat graphs
arun-sub/gatk
Official code repository for GATK versions 4 and up
arun-sub/GenomeWorks
SDK for GPU accelerated genome assembly and analysis
arun-sub/GKL
Accelerated kernel library for genomics
arun-sub/helen
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
arun-sub/htslib
C library for high-throughput sequencing data formats
arun-sub/Jellyfish
A fast multi-threaded k-mer counter
arun-sub/KMC
Fast and frugal disk based k-mer counter
arun-sub/lapidary
Creating beautiful gem5 simulations
arun-sub/medaka
Sequence correction provided by ONT Research
arun-sub/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
arun-sub/minimap2-acceleration
Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository
arun-sub/nanopolish
Signal-level algorithms for MinION data
arun-sub/plink-ng
A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.
arun-sub/racon
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
arun-sub/shasta
De novo assembly from Oxford Nanopore reads.
arun-sub/spoa
SIMD partial order alignment tool/library
arun-sub/TBSignatureProfiler
Profile RNA-Seq Data Using TB Pathway Signatures
arun-sub/Trans-Omics-Acceleration-Library