wtsi-npg/npg_seq_pipeline

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Language
Perl
Created almost 10 years ago
Updated 2 months ago

wtsi-npg/npg_seq_pipeline

wtsi-npg

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Processing and analysis of data coming from Illumina sequencing machines

illumina2bam

Generate and process BAM files from Illumina sequencing instrument files

baton

iRODS client programs and API

bambi

Process Illumina instrument data into SAM/BAM/CRAM files.

Percolate

A parallel workflow management application.

npg_qc

QC checks and metrics for Illumina NGS data

genotyping

Components of the WTSI genotype analysis pipeline.

npg_ranger

NGS data streaming (sam, bam, cram, vcf) - pre-production

perl-irods-wrap

Perl iRODS Client Wrapper Library

Gftools

A set of utilities to handle individual-level genotype data files

p4

Process and Pipe Pipeline Panacea

genotype-call

Explore the contents of Illumina's binary Genotype Call files

bcviz

JavaScript visualisation for bamcheck file format

npg_tracking

WTSI Illumina sequencing instruments (HiSeq, MiSeq, GA) tracking

npg_docker

Prototypes of Docker-contained Pipelines

ml_warehouse

Perl DBIx binding to a warehouse housing data from multiple LIM systems

Illuminus

A genotype calling algorithm for the Illumina BeadArray platform

npg_porch

irods-metadata

Description of a subset of metadata used in WTSI iRODS

perl-dnap-utilities

WTSI DNA Pipelines Perl Utility Library

pb_calibration

Filter and calibration programs for Illumina BAM files

samtools-patches

patch files for various releases of samtools

valet

Automated data mangement for Oxford Nanopore DNA sequencing instruments

npg_irods

Tools for managing HTS (BAM and CRAM) format files in iRODS.

npg_conda

NPG Conda recipes and tools

samtools_container

Scripts to create a docker container for samtools

partisan

A Python client API for iRODS

simtools

Program to create and process SIM files

git-pom-version

Updates the version of Maven pom files using "git describe"

npg-irods-python

Applications for the management of data and metadata in iRODS

containers

Singularity and Docker material

npg_qc_utils

C programs extracted from npg_qc