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1. mskcc/vcf2maf mskcc/vcf2maf Public

   Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

   Perl 421 219

2. Azure stack for Illumina Dragen PAYG Azure stack for Illumina Dragen PAYG

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   ### Purpose

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   Build an Azure stack to operate NP-series VMs on Azure with Dragen's pay-as-you-go (PAYG) license.

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   ### Prerequisites

3. Docker portability vs performance Docker portability vs performance

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   # Benchmarking Docker Base Images: Universal Portability vs. Native Microarchitecture Tuning

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   When deploying production bioinformatics pipelines in containers, does the choice of base operating system (**CachyOS-v3** vs. **Ubuntu 26.04 LTS** vs. **AlmaLinux 10 Kitten**) significantly impact end-to-end performance? And more critically: **can high performance be achieved without sacrificing the universal portability that containerization is meant to guarantee?**

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   Specialized distributions such as CachyOS optimize userland binaries and shared libraries for advanced x86 microarchitectures (e.g. `x86-64-v3` with AVX2/BMI1/BMI2/FMA or `x86-64-v4` with AVX-512). However, deploying an architecture-specific base image creates a non-portable container that will terminate immediately with `SIGILL` (Illegal Instruction) when executed on older CPUs or standard cloud compute instances (e.g., legacy AWS EC2, Google Cloud N1, or heterogeneous on-premise HPC clusters).

4. dotfiles dotfiles Public

   My bash dotfiles

   Shell