FelixKrueger

TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

SNPsplit

Allele-specific alignment sorting

Sherman

A simple Bisulfite FastQ Read Simulator (BiQRS)

nextflow_pipelines

The set of NGS processing pipelines used at Babraham

Umi-Grinder

The use of UMIs for sequencing becomes more and more frequently used so we need to take them into consideration when deduplicating data aligning to the same positions

reStrainingOrder

A little QC tool that attempts to predict the genotype of mouse samples used, based on prior knowledge of high-quality SNPs from the Mouse Genomes Project

IMPLICON

A processing guide for IMPLICON data (bisulfite amplicon data for imprinted loci)

scRepeats

Custom script(s) for the processing of files for single-cell repeat analysis

TrAEL-seq

A collection of software used for the TrAEL-seq manuscript

aws_training_images

A set of build scripts to generate AWS instances ready to run our training courses

bioconda-recipes

Conda recipes for the bioconda channel.

Complete-Python-3-Bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

deduplicate_by_sequence

This script reads paired-end BAM files, and deduplicates alignments based purely on exact matches of the first 50bp of both reads.

fetchngs

Pipeline to fetch metadata and raw FastQ files from public and private databases. Modifying pigz execution

GEO-submissions

illuminaprocessing

The scripts for doing automated run processing from our sequencing facility

L1EM

Estimate locus specific human LINE-1 expression.

lightweight-template

A minimal Nextflow pipeline that works with @nf-core modules.

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

MultiQC_TestData

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

nf-core-modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

nf-WGS

A simple workflow to get alignments done. Testing subworkflow setup

RinseRepeat

A collection of repetitive things...

simplealign

minimal WGS workflow with nf-core tools 2.9dev

Singularity_Test2

conda test

SlamDunk_Shub

Trying to get Slamdunk to work on CentOS 6

subset10xbam

A tool to extract subsets of data from the tagged BAM file generated by CellRanger

test-datasets

Test data to be used for automated testing with the nf-core pipelines

travisTest

testing_travis