Pinned Repositories
BabrahamLinkON
Pipeline for processing VDJ-Seq data
Bismark
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
IMPLICON
A processing guide for IMPLICON data (bisulfite amplicon data for imprinted loci)
nextflow_pipelines
The set of NGS processing pipelines used at Babraham
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
scRepeats
Custom script(s) for the processing of files for single-cell repeat analysis
Sherman
A simple Bisulfite FastQ Read Simulator (BiQRS)
SNPsplit
Allele-specific alignment sorting
TrimGalore
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
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
FelixKrueger's Repositories
FelixKrueger/TrimGalore
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
FelixKrueger/Bismark
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
FelixKrueger/SNPsplit
Allele-specific alignment sorting
FelixKrueger/Sherman
A simple Bisulfite FastQ Read Simulator (BiQRS)
FelixKrueger/nextflow_pipelines
The set of NGS processing pipelines used at Babraham
FelixKrueger/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
FelixKrueger/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
FelixKrueger/scRepeats
Custom script(s) for the processing of files for single-cell repeat analysis
FelixKrueger/IMPLICON
A processing guide for IMPLICON data (bisulfite amplicon data for imprinted loci)
FelixKrueger/TrAEL-seq
A collection of software used for the TrAEL-seq manuscript
FelixKrueger/aws_training_images
A set of build scripts to generate AWS instances ready to run our training courses
FelixKrueger/bioconda-recipes
Conda recipes for the bioconda channel.
FelixKrueger/Complete-Python-3-Bootcamp
Course Files for Complete Python 3 Bootcamp Course on Udemy
FelixKrueger/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.
FelixKrueger/fetchngs
Pipeline to fetch metadata and raw FastQ files from public and private databases. Modifying pigz execution
FelixKrueger/GEO-submissions
FelixKrueger/illuminaprocessing
The scripts for doing automated run processing from our sequencing facility
FelixKrueger/L1EM
Estimate locus specific human LINE-1 expression.
FelixKrueger/lightweight-template
A minimal Nextflow pipeline that works with @nf-core modules.
FelixKrueger/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
FelixKrueger/MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
FelixKrueger/nf-core-modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
FelixKrueger/nf-WGS
A simple workflow to get alignments done. Testing subworkflow setup
FelixKrueger/RinseRepeat
A collection of repetitive things...
FelixKrueger/simplealign
minimal WGS workflow with nf-core tools 2.9dev
FelixKrueger/Singularity_Test2
conda test
FelixKrueger/SlamDunk_Shub
Trying to get Slamdunk to work on CentOS 6
FelixKrueger/subset10xbam
A tool to extract subsets of data from the tagged BAM file generated by CellRanger
FelixKrueger/test-datasets
Test data to be used for automated testing with the nf-core pipelines
FelixKrueger/travisTest
testing_travis