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    39 repositories

    • nf-core_sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •430•1•0•0•Updated Mar 5, 2025Mar 5, 2025

    • aladdin-shotgun

      Public
      Python
      •
      MIT License
      •2•1•8•0•Updated Mar 5, 2025Mar 5, 2025

    • aladdin-miqScoreShotgun

      Public
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

    • nf-core-Sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •430•0•0•0•Updated Feb 26, 2025Feb 26, 2025

    • aladdin-rnaseq

      Public
      Public repository for RNAseq pipeline to be run on Aladdin platform
      Python
      •
      MIT License
      •0•3•2•0•Updated Feb 22, 2025Feb 22, 2025

    • service-pipeline-documentation

      Public
      Public repository to educate customers about bioinformatics pipelines and reports for services we offer
      HTML
      •1•4•1•0•Updated Jan 3, 2025Jan 3, 2025

    • VirSieve

      Public
      Run manager for the VirSieve Pipeline by Zymo Research
      Python
      •2•5•2•0•Updated Dec 16, 2024Dec 16, 2024

    • aladdin-miqScore16S

      Public
      Nextflow pipeline that calculates MIQ score. Compatible with Aladdin platform
      Nextflow
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 12, 2024Dec 12, 2024

    • miqScore16SPublic

      Public
      Repo for public-facing 16s miq score
      HTML
      •
      GNU General Public License v3.0
      •4•8•6•2•Updated Dec 6, 2024Dec 6, 2024

    • VirSieveVEP

      Public
      VEP functionality and called variant analysis for the VirSieve Pipeline by Zymo Research
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • VirSieveGATK

      Public
      GATK functionality for the VirSieve Pipeline by Zymo Research
      Python
      •
      GNU General Public License v3.0
      •1•1•1•0•Updated Dec 4, 2024Dec 4, 2024

    • virsievefreyja

      Public
      Freyja portion of the virsieve pipeline
      Python
      •1•0•2•0•Updated Dec 3, 2024Dec 3, 2024

    • VirSieveAlign

      Public
      Alignment and related functionality for the VirSieve Pipeline by Zymo Research
      Python
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Nov 27, 2024Nov 27, 2024

    • SquidSuite

      Public
      0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • aladdin-smrnaseq

      Public
      Public repository for smRNAseq pipeline compatible with Aladdin platform
      Python
      •
      MIT License
      •0•2•0•1•Updated Sep 23, 2024Sep 23, 2024

    • io-pipeline-shotgun

      Public
      Processing pipeline for Shotgun data of the Integrated Omics Team
      Nextflow
      •
      MIT License
      •2•0•1•0•Updated Sep 23, 2024Sep 23, 2024

    • pipeline-resources

      Public
      Repository for resources and documentation files of Zymo bioinformatics pipelines
      HTML
      •1•2•0•0•Updated Sep 16, 2024Sep 16, 2024

    • wgbs-genetic-variants

      Public
      Instructions for genetic variant detection from whole genome bisulfite sequencing (WGBS) data
      0•3•0•0•Updated Sep 12, 2024Sep 12, 2024

    • docker-bcl2fastq

      Public
      Docker container for Illumina bcl2fastq
      C
      •14•10•0•0•Updated Aug 7, 2024Aug 7, 2024

    • figaro

      Public
      An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
      Python
      •
      GNU General Public License v3.0
      •26•87•28•2•Updated Jul 12, 2024Jul 12, 2024

    • ncbi-pmc-scraper

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jul 7, 2024Jul 7, 2024

    • docker-bcl-convert

      Public
      Docker container for bcl-convert, an Illumina demultiplexing program
      Dockerfile
      •1•2•0•0•Updated May 8, 2024May 8, 2024

    • miqScoreShotgunPublic

      Public
      Repo for public-facing shotgun MIQ score
      HTML
      •
      GNU General Public License v3.0
      •6•7•1•4•Updated Feb 23, 2024Feb 23, 2024

    • zymoTransmit

      Public
      Python script to facilitate uploading COVID-19 test results to departments of health
      Python
      •
      GNU General Public License v3.0
      •2•8•1•1•Updated Oct 18, 2023Oct 18, 2023

    • aladdin-bisulfitebolt

      Public
      Python
      •0•1•0•0•Updated Sep 25, 2023Sep 25, 2023

    • KingFisher.Flex.R2132.Script

      Public
      Script for the Zymo R2132 Kit on the KingFisher Flex Platform
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 18, 2023Sep 18, 2023

    • miqScoreGutStandardShotgun

      Public
      Public repo for the MIQ score system for analyzing Zymo Gut Standard reads
      Python
      •
      GNU General Public License v3.0
      •1•0•2•2•Updated Jul 6, 2023Jul 6, 2023

    • aladdin-integration

      Public
      Documentation and tools to develop pipelines that can be run on Aladdin
      0•2•0•0•Updated Jun 13, 2023Jun 13, 2023

    • VirSieveIVar

      Public
      iVar functionality for the VirSieve Pipeline by Zymo Research
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 9, 2021Apr 9, 2021

    • KingFisher.Flex.QuickDNAFecal

      Public
      Customer KingFisher script from Lallemand Health Solutions
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 10, 2020Sep 10, 2020