Skip to content

Open-Omics-Acceleration-Framework-2.0
Compare
Choose a tag to compare
@sanchit-misra sanchit-misra released this 22 Nov 14:50
· 114 commits to main since this release
2.0
0eaf428
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

This v2.0 release adds the accelerated version of following new pipelines and corresponding tools.

  • Containerized AlphaFold2-based pipeline for protein folding that takes protein sequences as input and outputs predicted protein structures. It consists of

    • Open-Omics-AlphaFold: a PyTorch implementation of AlphaFold2 (v.2.2.2) monomer accelerated using 4th generation Intel® Xeon® CPU.
    • Hmmer and HH-suite accelerated through 256- and 512-bit SIMD instructions (AVX2, AVX512) available on modern x86 CPUs.
    • Efficient load balanced folding of multiple proteins in parallel on a dual-socket CPU.
    • A docker file for seamless installation and execution.
    • Can perform folding on proteins of length up to ~9k residues on a 1 TB memory machine.
    • To the best of our knowledge, faster than any prior CPU/GPU implementation for folding a set of proteins.

  • Containerized DeepVariant-based variant calling (fq2vcf) pipeline that takes paired fastq.gz files as input and outputs vcf file. It achieves efficient performance across multiple CPU nodes and consists of

    • BWA-MEM2: an architecture-efficient version of BWA-MEM that is 1.8-3.0 times faster.
    • SAMtools sort utility for sorting SAM/BAM files.
    • Open-Omics-DeepVariant: A new version of DeepVariant v1.5.0 accelerated using 4th generation Intel® Xeon® CPU.
    • A distributed memory framework that achieves excellent scaling for this pipeline across several CPU nodes.
    • To the best of our knowledge, faster than any prior CPU/GPU implementation for 30x WGS dataset.

  • A fq2sortedbam pipeline accelerated using modern CPUs that takes read fastq files as input and outputs a sorted BAM file. It consists of

    • BWA-MEM2: an architecture-efficient version of BWA-MEM that is 1.8-3.0 times faster.
    • SAMtools sort utility for sorting SAM/BAM files.
Assets 3
Loading