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    30 repositories

    • smrtino

      Public
      Run pipeline for PacBio Sequel SMRT cells
      Python
      •
      Other
      •0•0•2•0•Updated Dec 23, 2024Dec 23, 2024

    • illuminatus

      Public
      The all-knowing, all-seeing, enlightened pipeline for Illumina run processing.
      Python
      •
      Other
      •1•2•0•0•Updated Dec 19, 2024Dec 19, 2024

    • Analysis-Driver

      Public
      Pipelines for Illumina HiSeqX demultiplexing, sequence QC and variant calling.
      Python
      •0•8•12•1•Updated Dec 10, 2024Dec 10, 2024

    • hesiod

      Public
      Reports on your Promethion (or other NanoPore) data.
      Python
      •
      Other
      •0•1•2•0•Updated Dec 10, 2024Dec 10, 2024

    • bashmocker

      Public
      A Python helper for unit testing shell scripts.
      Python
      •
      Other
      •0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • snakemake

      Public
      Fork of Snakemake for adding patches and fixes for EdGe
      HTML
      •
      MIT License
      •562•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • NERC_EcologicalGenomics

      Public
      Bioinformatics Workflow for NERC Ecological Genomics training 2023
      0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • transfer_test_maker

      Public
      Helps to make pathological test cases for FTP downloads
      Python
      •0•0•0•0•Updated Oct 16, 2023Oct 16, 2023

    • clarity_scripts

      Public
      API and EPP scripts
      Python
      •
      MIT License
      •0•1•15•3•Updated Oct 3, 2023Oct 3, 2023

    • MultiQC_EdGen

      Public
      Plugin for MultiQC specific to use with Illuminatus pipeline
      Python
      •
      Other
      •0•0•0•0•Updated Oct 3, 2022Oct 3, 2022

    • MultiQC

      Public
      Edinburgh Genomics fork of the MultiQC project. You probably want to use the upstream version - fixes from here will be contributed back there.
      Python
      •
      GNU General Public License v3.0
      •608•0•0•0•Updated Aug 24, 2022Aug 24, 2022

    • EGCG-Project-Management

      Public
      Tools for managing the data generated by EdinburghGenomics/Analysis-Driver, including review, delivery and deletion.
      Python
      •
      Other
      •0•1•9•1•Updated Jun 21, 2022Jun 21, 2022

    • training_on_cloud

      Public
      Scripts and configuration and notes for running training desktops on cloud
      Python
      •
      MIT License
      •0•2•0•0•Updated May 26, 2022May 26, 2022

    • pyclarity-lims

      Public
      Python interface to the GenoLogics LIMS server via its REST API.
      Python
      •
      MIT License
      •53•11•6•0•Updated Mar 30, 2022Mar 30, 2022

    • blobtools

      Public
      Application for the visualisation of draft genome assemblies and general QC
      Python
      •
      GNU General Public License v3.0
      •44•0•0•0•Updated Dec 21, 2021Dec 21, 2021

    • Reporting-App

      Public
      A Flask web app for presenting bcl2fastq and variant calling performance reports from Analysis-Driver
      Python
      •
      Other
      •1•4•11•1•Updated May 6, 2021May 6, 2021

    • EGCG-Core

      Public
      Shared functionality across EGCG projects
      Python
      •
      Other
      •2•0•0•2•Updated Mar 25, 2021Mar 25, 2021

    • sf2-webapp

      Public
      Online SF2 web application
      JavaScript
      •
      MIT License
      •0•0•0•9•Updated Sep 10, 2020Sep 10, 2020

    • minion_qc

      Public
      Quality control for MinION sequencing data
      R
      •
      MIT License
      •41•1•0•0•Updated Aug 8, 2019Aug 8, 2019

    • genologics_sql

      Public
      Python interface for the Genologics Postgres database.
      Python
      •
      MIT License
      •9•0•0•0•Updated Jul 4, 2019Jul 4, 2019

    • well_duplicates

      Public
      localised duplicate detection on patterned flow cells
      Python
      •
      Other
      •2•10•0•0•Updated Feb 27, 2019Feb 27, 2019

    • Small_tools

      Public
      Python
      •0•0•0•0•Updated Jan 24, 2019Jan 24, 2019

    • Fastq-Filterer

      Public
      Filtering tiles and short reads from paired-end fastq files.
      C
      •
      MIT License
      •0•0•0•0•Updated Jun 4, 2018Jun 4, 2018

    • MultiQC_TestData

      Public
      Test data for MultiQC. See https://github.com/ewels/MultiQC
      HTML
      •
      MIT License
      •146•0•0•0•Updated Jul 21, 2017Jul 21, 2017

    • slurm_tools

      Public
      Some scripts we're using with the SLURM job scheduler
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated May 17, 2017May 17, 2017

    • RADmapper

      Public
      Set of scripts to create denovo consensus and map the read back
      Python
      •
      MIT License
      •2•0•0•0•Updated Nov 18, 2016Nov 18, 2016

    • clarity_view

      Public archive
      Small web app to offer alternative views of clarity LIMS
      HTML
      •0•0•0•0•Updated Aug 19, 2016Aug 19, 2016

    • report_generation

      Public archive
      suite of script for simple generation of report
      Python
      •0•0•0•0•Updated Jun 30, 2016Jun 30, 2016

    • seqtk

      Public
      Toolkit for processing sequences in FASTA/Q formats
      C
      •
      MIT License
      •307•0•0•0•Updated Feb 9, 2016Feb 9, 2016

    • Process-Trigger

      Public archive
      Bash helper scripts for Analysis-Driver. Scans for new Illumina HiSeq datasets and calls Analysis-Driver. (deprecated)
      Shell
      •0•0•0•0•Updated Aug 5, 2015Aug 5, 2015