felixkrueger Goto Github PK

aws_training_images

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

babrahamlinkon

Pipeline for processing VDJ-Seq data

bioconda-recipes

Conda recipes for the bioconda channel.

bismark

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

bismarkmultimappinglocations

This is a side-project of Bismark whose aim is to output multiply mapping read positions without any of the methylation specific features.

camhack2017

Project page for the Cambridge Bioinformatics Hackathon, @Craik Marshall Building, Downing Site, Sept 25-27, 2017

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

implicon

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

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

newdocs

fine

nextflow_pipelines

The set of NGS processing pipelines used at Babraham

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

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

rinserepeat

A collection of repetitive things...

screpeats

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

seqmage

A generic sequence retrieval tool for genomic coordinates

sherman

A simple Bisulfite FastQ Read Simulator (BiQRS)

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

snpsplit

Allele-specific alignment sorting

subset10xbam

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