Pinned Repositories
Analysis-Driver
Pipelines for Illumina HiSeqX demultiplexing, sequence QC and variant calling.
clarity_scripts
API and EPP scripts
EGCG-Core
Shared functionality across EGCG projects
EGCG-Project-Management
Tools for managing the data generated by EdinburghGenomics/Analysis-Driver, including review, delivery and deletion.
hesiod
Reports on your Promethion (or other NanoPore) data.
illuminatus
The all-knowing, all-seeing, enlightened pipeline for Illumina run processing.
pyclarity-lims
Python interface to the GenoLogics LIMS server via its REST API.
Reporting-App
A Flask web app for presenting bcl2fastq and variant calling performance reports from Analysis-Driver
training_on_cloud
Scripts and configuration and notes for running training desktops on cloud
well_duplicates
localised duplicate detection on patterned flow cells
Edinburgh Genomics's Repositories
EdinburghGenomics/pyclarity-lims
Python interface to the GenoLogics LIMS server via its REST API.
EdinburghGenomics/well_duplicates
localised duplicate detection on patterned flow cells
EdinburghGenomics/Analysis-Driver
Pipelines for Illumina HiSeqX demultiplexing, sequence QC and variant calling.
EdinburghGenomics/Reporting-App
A Flask web app for presenting bcl2fastq and variant calling performance reports from Analysis-Driver
EdinburghGenomics/illuminatus
The all-knowing, all-seeing, enlightened pipeline for Illumina run processing.
EdinburghGenomics/training_on_cloud
Scripts and configuration and notes for running training desktops on cloud
EdinburghGenomics/clarity_scripts
API and EPP scripts
EdinburghGenomics/EGCG-Project-Management
Tools for managing the data generated by EdinburghGenomics/Analysis-Driver, including review, delivery and deletion.
EdinburghGenomics/hesiod
Reports on your Promethion (or other NanoPore) data.
EdinburghGenomics/minion_qc
Quality control for MinION sequencing data
EdinburghGenomics/EGCG-Core
Shared functionality across EGCG projects
EdinburghGenomics/Fastq-Filterer
Filtering tiles and short reads from paired-end fastq files.
EdinburghGenomics/MultiQC_EdGen
Plugin for MultiQC specific to use with Illuminatus pipeline
EdinburghGenomics/NERC_EcologicalGenomics
Bioinformatics Workflow for NERC Ecological Genomics training 2023
EdinburghGenomics/bashmocker
A Python helper for unit testing shell scripts.
EdinburghGenomics/blobtools
Application for the visualisation of draft genome assemblies and general QC
EdinburghGenomics/clarity_view
Small web app to offer alternative views of clarity LIMS
EdinburghGenomics/genologics_sql
Python interface for the Genologics Postgres database.
EdinburghGenomics/MultiQC
Edinburgh Genomics fork of the MultiQC project. You probably want to use the upstream version - fixes from here will be contributed back there.
EdinburghGenomics/MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
EdinburghGenomics/Process-Trigger
Bash helper scripts for Analysis-Driver. Scans for new Illumina HiSeq datasets and calls Analysis-Driver. (deprecated)
EdinburghGenomics/RADmapper
Set of scripts to create denovo consensus and map the read back
EdinburghGenomics/report_generation
suite of script for simple generation of report
EdinburghGenomics/seqtk
Toolkit for processing sequences in FASTA/Q formats
EdinburghGenomics/sf2-webapp
Online SF2 web application
EdinburghGenomics/slurm_tools
Some scripts we're using with the SLURM job scheduler
EdinburghGenomics/Small_tools
EdinburghGenomics/smrtino
Run pipeline for PacBio Sequel SMRT cells
EdinburghGenomics/snakemake
Fork of Snakemake for adding patches and fixes for EdGe
EdinburghGenomics/transfer_test_maker
Helps to make pathological test cases for FTP downloads