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@wtsi-npg Wellcome Sanger Institute - NPG

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    79 repositories

    • npg_tracking

      Public
      WTSI Illumina sequencing instruments (HiSeq, MiSeq, GA) tracking
      Perl
      •19•3•12•2•Updated Oct 4, 2024Oct 4, 2024

    • perl-irods-wrap

      Public
      Perl iRODS Client Wrapper Library
      irodsperl
      Perl
      •20•4•12•0•Updated Oct 4, 2024Oct 4, 2024

    • npg-python-lib

      Public
      A library of Python functions and classes common to NPG applications
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 4, 2024Oct 4, 2024

    • p4

      Public
      Process and Pipe Pipeline Panacea
      Perl
      •15•3•8•9•Updated Oct 2, 2024Oct 2, 2024

    • npg_langqc

      Public
      Python
      •
      GNU General Public License v3.0
      •5•0•2•2•Updated Oct 2, 2024Oct 2, 2024

    • npg_porch_cli

      Public
      A command-line client to enable communication with the npg_porch API.
      Python
      •3•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • npg-irods-python

      Public
      Applications for the management of data and metadata in iRODS
      Python
      •
      GNU General Public License v3.0
      •7•1•1•2•Updated Oct 1, 2024Oct 1, 2024

    • npg_ml_warehouse

      Public
      Analysis results loader for the multi-lims warehouse, see ml_warehouse project for the warehouse details.
      Perl
      •13•0•9•1•Updated Oct 1, 2024Oct 1, 2024

    • ml_warehouse

      Public
      Perl DBIx binding to a warehouse housing data from multiple LIM systems
      Perl
      •14•3•1•0•Updated Oct 1, 2024Oct 1, 2024

    • npg_notifications

      Public
      Python
      •3•0•1•0•Updated Oct 1, 2024Oct 1, 2024

    • npg_seq_pipeline

      Public
      Processing and analysis of data coming from Illumina sequencing machines
      Perl
      •17•9•23•8•Updated Oct 1, 2024Oct 1, 2024

    • npg_qc

      Public
      QC checks and metrics for Illumina NGS data
      Perl
      •17•5•20•2•Updated Oct 1, 2024Oct 1, 2024

    • npg_conda

      Public
      NPG Conda recipes and tools
      Shell
      •15•1•10•0•Updated Oct 1, 2024Oct 1, 2024

    • npg_id_generation

      Public
      Python
      •
      GNU General Public License v3.0
      •5•0•1•0•Updated Oct 1, 2024Oct 1, 2024

    • perl-dnap-utilities

      Public
      WTSI DNA Pipelines Perl Utility Library
      Perl
      •
      GNU General Public License v3.0
      •11•2•0•0•Updated Oct 1, 2024Oct 1, 2024

    • genotyping

      Public
      Components of the WTSI genotype analysis pipeline.
      Perl
      •7•5•11•1•Updated Oct 1, 2024Oct 1, 2024

    • bambi

      Public
      Process Illumina instrument data into SAM/BAM/CRAM files.
      bam-filesbioinformaticsilluminahtslib
      C
      •
      GNU Affero General Public License v3.0
      •15•9•8•0•Updated Oct 1, 2024Oct 1, 2024

    • samtools_container

      Public
      Scripts to create a docker container for samtools
      Shell
      •7•1•3•0•Updated Oct 1, 2024Oct 1, 2024

    • npg_seq_common

      Public
      Utilities for handling NGS data
      Perl
      •15•0•1•0•Updated Oct 1, 2024Oct 1, 2024

    • bcviz

      Public
      JavaScript visualisation for bamcheck file format
      JavaScript
      •
      Other
      •7•3•6•0•Updated Oct 1, 2024Oct 1, 2024

    • build-irods-client-action

      Public
      GitHub Action providing a custom Docker container in which to build iRODS clients
      C
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • containers

      Public
      Singularity and Docker material
      Dockerfile
      •6•1•8•0•Updated Sep 30, 2024Sep 30, 2024

    • baton

      Public
      iRODS client programs and API
      C
      •
      GNU General Public License v2.0
      •19•19•11•0•Updated Sep 27, 2024Sep 27, 2024

    • irods-metadata

      Public
      Description of a subset of metadata used in WTSI iRODS
      2•2•0•0•Updated Sep 24, 2024Sep 24, 2024

    • npg_irods

      Public
      Tools for managing HTS (BAM and CRAM) format files in iRODS.
      Perl
      •
      GNU General Public License v3.0
      •17•2•17•2•Updated Sep 24, 2024Sep 24, 2024

    • partisan

      Public
      A Python client API for iRODS
      Python
      •
      GNU General Public License v3.0
      •5•1•1•0•Updated Sep 20, 2024Sep 20, 2024

    • irods_development_environment

      Public
      Dockerfile
      •
      BSD 3-Clause "New" or "Revised" License
      •11•0•0•0•Updated Sep 13, 2024Sep 13, 2024

    • sqyrrl

      Public
      Sqyrrl - an HTTP server for files hosted in iRODS
      Go
      •
      GNU General Public License v3.0
      •4•0•2•0•Updated Sep 10, 2024Sep 10, 2024

    • valet

      Public
      Automated data mangement for Oxford Nanopore DNA sequencing instruments
      nanoporebatonirodsoxford-nanoporegridionextendopromethion
      Go
      •
      GNU General Public License v3.0
      •4•2•4•0•Updated Sep 10, 2024Sep 10, 2024

    • extendo

      Public
      An extension to baton providing a Go API for iRODS (Integrated Rule-Oriented Data System)
      batonirods
      Go
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 4, 2024Sep 4, 2024