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    21 repositories

    • vcflib

      Public
      C++ library and cmdline tools for parsing and manipulating VCF files
      C++
      •
      MIT License
      •223•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • savR

      Public
      R
      •3•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • bcftools

      Public
      This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/i…
      C
      •
      Other
      •267•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • xDrip

      Public
      Nightscout version of xDrip+
      Java
      •
      GNU General Public License v3.0
      •1.2k•0•0•0•Updated Jan 15, 2022Jan 15, 2022

    • SARS-CoV-2_PRJNA612766

      Public
      Analysis of early Wuhan SARS-CoV-2 sequences from deleted SRA BioProject PRJNA612766
      HTML
      •13•0•0•0•Updated Jun 28, 2021Jun 28, 2021

    • sambamba

      Public
      Tools for working with SAM/BAM data
      D
      •
      GNU General Public License v2.0
      •104•0•0•0•Updated Jun 16, 2021Jun 16, 2021

    • nextclade

      Public
      Viral genome alignment, clade assignment, mutation calling, and quality checks
      TypeScript
      •
      MIT License
      •66•0•0•0•Updated Apr 30, 2021Apr 30, 2021

    • taxonkit

      Public
      A Practical and Efficient NCBI Taxonomy Toolkit
      Go
      •
      MIT License
      •30•0•0•0•Updated Apr 16, 2021Apr 16, 2021

    • Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273

      Public
      RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical…
      475•0•0•0•Updated Apr 4, 2021Apr 4, 2021

    • bedtools2

      Public
      bedtools - the swiss army knife for genome arithmetic
      C
      •
      MIT License
      •295•0•0•0•Updated Feb 26, 2021Feb 26, 2021

    • parkour

      Public
      An open-source Laboratory Information Management System (LIMS) for Next-Generation Sequencing (NGS)
      JavaScript
      •
      GNU General Public License v3.0
      •15•0•0•0•Updated Feb 2, 2021Feb 2, 2021

    • fieldbioinformatics

      Public
      The ARTIC field bioinformatics pipeline
      Python
      •
      MIT License
      •91•0•0•0•Updated Dec 16, 2020Dec 16, 2020

    • ont_fast5_api

      Public
      Oxford Nanopore Technologies fast5 API software
      Python
      •
      Other
      •30•0•0•0•Updated Sep 15, 2020Sep 15, 2020

    • ncov

      Public
      Nextstrain build for novel coronavirus (nCoV)
      Python
      •
      MIT License
      •409•0•0•0•Updated Aug 14, 2020Aug 14, 2020

    • augur

      Public
      Pipeline components for real-time phylodynamic analysis
      Python
      •
      GNU Affero General Public License v3.0
      •136•0•0•0•Updated Aug 14, 2020Aug 14, 2020

    • auspice

      Public
      Web app for visualizing pathogen evolution
      JavaScript
      •
      GNU Affero General Public License v3.0
      •169•0•0•0•Updated Aug 14, 2020Aug 14, 2020

    • Filtlong

      Public
      quality filtering tool for long reads
      C++
      •
      GNU General Public License v3.0
      •30•0•0•0•Updated May 27, 2020May 27, 2020

    • kableExtra

      Public
      Construct Complex Table with knitr::kable() + pipe.
      R
      •
      Other
      •152•0•0•0•Updated Sep 6, 2019Sep 6, 2019

    • dfn_rstudio

      Public
      WINST-Script-Paket für die Verteilung des Programms RStudio per OPSI
      Shell
      •1•0•0•0•Updated May 10, 2019May 10, 2019

    • Krona

      Public
      Interactively explore metagenomes and more from a web browser.
      JavaScript
      •107•0•0•0•Updated Sep 4, 2018Sep 4, 2018

    • pyfaidx

      Public
      Efficient pythonic random access to fasta subsequences
      Python
      •
      Other
      •76•0•0•0•Updated Jul 25, 2017Jul 25, 2017
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