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analysis-driver

Pipelines for Illumina HiSeqX demultiplexing, sequence QC and variant calling.

bashmocker

A Python helper for unit testing shell scripts.

blobtools

Application for the visualisation of draft genome assemblies and general QC

clarity_scripts

API and EPP scripts

clarity_view

Small web app to offer alternative views of clarity LIMS

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.

fastq-filterer

Filtering tiles and short reads from paired-end fastq files.

genologics_sql

Python interface for the Genologics Postgres database.

hesiod

Reports on your Promethion (or other NanoPore) data.

illuminatus

The all-knowing, all-seeing, enlightened pipeline for Illumina run processing.

minion_qc

Quality control for MinION sequencing data

multiqc

Edinburgh Genomics fork of the MultiQC project. You probably want to use the upstream version - fixes from here will be contributed back there.

multiqc_edgen

Plugin for MultiQC specific to use with Illuminatus pipeline

multiqc_testdata

Test data for MultiQC. See https://github.com/ewels/MultiQC

process-trigger

Bash helper scripts for Analysis-Driver. Scans for new Illumina HiSeq datasets and calls Analysis-Driver. (deprecated)

pyclarity-lims

Python interface to the GenoLogics LIMS server via its REST API.

radmapper

Set of scripts to create denovo consensus and map the read back

report_generation

suite of script for simple generation of report

reporting-app

A Flask web app for presenting bcl2fastq and variant calling performance reports from Analysis-Driver

seqtk

Toolkit for processing sequences in FASTA/Q formats

sf2-webapp

Online SF2 web application

slurm_tools

Some scripts we're using with the SLURM job scheduler

small_tools

smrtino

Run pipeline for PacBio Sequel SMRT cells

snakemake

Fork of Snakemake for adding patches and fixes for EdGe

training_on_cloud

Scripts and configuration and notes for running training desktops on cloud

transfer_test_maker

Helps to make pathological test cases for FTP downloads

well_duplicates

localised duplicate detection on patterned flow cells