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@serratus-bio Serratus

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    27 repositories

    • open-virome

      Public
      monorepo for data explorer UI and APIs
      TypeScript
      •
      GNU Affero General Public License v3.0
      •0•0•30•0•Updated Nov 29, 2024Nov 29, 2024

    • logan-backend

      Public
      JavaScript
      •2•0•2•0•Updated Oct 22, 2024Oct 22, 2024

    • pangenome

      Public
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Oct 14, 2024Oct 14, 2024

    • serratus.io

      Public
      Front-end code for Serratus project website
      reactjsd3jstailwindcssaws-amplify
      TypeScript
      •
      GNU Affero General Public License v3.0
      •11•11•30•7•Updated Jul 2, 2024Jul 2, 2024

    • biosample-sql

      Public
      making some sense out of biosample_set.xml.gz
      aws-lambdaaurora-serverless
      Python
      •
      GNU General Public License v3.0
      •0•2•1•0•Updated May 23, 2024May 23, 2024

    • serratus-geo-utils

      Public
      HTML
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Feb 13, 2024Feb 13, 2024

    • serratus-utils

      Public
      Small scripts that perform useful functions related to the serratus platform.
      JavaScript
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Nov 7, 2023Nov 7, 2023

    • serratus-summary-api

      Public
      serving Serratus summary data via a public API
      aws-elastic-beanstalkflask-sqlalchemyaurora-serverless
      Python
      •
      GNU Affero General Public License v3.0
      •5•0•4•0•Updated Oct 23, 2023Oct 23, 2023

    • bs2csv

      Public
      Python script to extract Biosample metadata to a csv file
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Oct 15, 2023Oct 15, 2023

    • serratus-summary-uploader

      Public
      parse and upload Serratus summary files to various AWS offerings via AWS Lambda
      aws-lambdaaws-athenaaws-auroraconcurrency
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Sep 10, 2023Sep 10, 2023

    • serratus-summary-utils

      Public
      JavaScript
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jun 9, 2023Jun 9, 2023

    • palmid-lambda

      Public
      AWS Lambda service for `palmid` R-package/container
      awslambdavirus
      Python
      •1•0•0•0•Updated Jun 5, 2023Jun 5, 2023

    • serratus-summary-api-debug

      Public
      serving Serratus summary data via a public API
      Python
      •
      GNU Affero General Public License v3.0
      •5•0•0•0•Updated May 29, 2023May 29, 2023

    • tantalus

      Public
      R Data Exploration for Serratus
      R
      •
      GNU General Public License v3.0
      •3•15•2•0•Updated Mar 29, 2023Mar 29, 2023

    • palmdb

      Public
      Database of virus RdRP barcode sequences
      Creative Commons Zero v1.0 Universal
      •5•0•0•0•Updated Jun 30, 2021Jun 30, 2021

    • serratus

      Public
      Archival Fork of the main Serratus repository.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •34•1•0•0•Updated Mar 14, 2021Mar 14, 2021

    • palmscan

      Public
      C++
      •
      GNU Affero General Public License v3.0
      •5•0•0•0•Updated Mar 11, 2021Mar 11, 2021

    • sraruninfo-sql

      Public
      making Serratus SRA run metadata query-able
      aws-lambdaaurora-serverless
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Feb 26, 2021Feb 26, 2021

    • serratus-summary-api-athena

      Public archive
      POC for serving Serratus summary data via AWS Athena
      expressjsaws-codepipelineaws-elastic-beanstalkaws-athena
      JavaScript
      •0•1•0•0•Updated Feb 13, 2021Feb 13, 2021

    • serratus-db

      Public
      code for Serratus database curation and API routes
      ef-coreaws-rds-postgres
      C#
      •0•0•2•0•Updated Dec 18, 2020Dec 18, 2020

    • diamond

      Public
      Accelerated BLAST compatible local sequence aligner.
      C++
      •
      GNU General Public License v3.0
      •182•0•0•0•Updated Aug 23, 2020Aug 23, 2020

    • nidhoggr

      Public
      Archival fork
      Python
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Aug 2, 2020Aug 2, 2020

    • serratus-batch-assembly

      Public
      Archive-Only. See: https://gitlab.pasteur.fr/rchikhi_pasteur/serratus-batch-assembly
      Jupyter Notebook
      •
      MIT No Attribution
      •0•0•0•0•Updated Jul 27, 2020Jul 27, 2020

    • darth

      Public
      Archival fork
      Pep8
      •0•0•0•0•Updated Jul 27, 2020Jul 27, 2020

    • serratus-api

      Public archive
      [deprecated] See serratus-summary-api repo for latest implementation.
      Python
      •0•0•0•0•Updated Jul 10, 2020Jul 10, 2020

    • samtools

      Public
      Tools (written in C using htslib) for manipulating next-generation sequencing data
      C
      •
      Other
      •580•0•0•0•Updated Jun 24, 2020Jun 24, 2020

    • seqkit

      Public
      A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
      Go
      •
      MIT License
      •159•0•0•0•Updated Jun 16, 2020Jun 16, 2020