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ampliconseq_qiime2

QIIME2 Metagenomics Amplicon Sequencing Pipeline

core

General Purpose code for the activities of the Bioinformatics Core

documentation

Documents and tutorials on the pipelines available at NIBSC Bioinformatics

gcp-env-scripts

bash scripts to create projects in GCP

gcp-scripts

Scripts for HPC-GCP data transfer

gcp-test

gcp-wiki

Repo for NIBSC GCP wiki

hpc_guide

Sphinx documentation to NIBSC HPC

humgen

Standard Pipeline for Human Genetics Analyses

metagenomics_mpa3

Shotgun Metagenomics Pipeline

microbiomemqc

Minimum Quality control for Microbiome data

modules

Nextflow DSL2 modules in use at NIBSC

modules2

nanoprofiler

Profiling Nanobodies sequencing libraries

nf-core-bagobugs

Nextflow DSL2 Pipeline for Shotgun Metagenomics Analysis

nf-core-buggybarcodes

nf-core-conva

Detection and quantification of gene copy numbers

nf-core-tools

Python package with helper tools for the nf-core community.

nf-core-viralevo

Bioinformatics analysis pipeline used to perform low-frequency variant calling for viral samples

nibscdoc

Package providing necessary templates for NIBSC Rmarkdown Reports

qc

Test directory for CNV workflow

rnaseqbenchmark

Repository for work on benchmarking RNAseq pipelines to be implemented in the next future

scoop

Another metagenomics pipeline with a cookery name. The pipeline is based on read classification (i.e. no assembly) and uses biobakery tools.

scranger

scRNAseq Pipeline running Cell Ranger and Seurat

singularity

Docker container with Singularity to be used for conversion of docker containers (as strange as it might sound.. yes)

testdata

small dataset used to run nextflow pipelines tests

variantviz

Collection of interoperable tools to create different visualisations of genetic variants in different organisms

viralevo