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Last pushed: 2 years ago
Short Description
NGSeasy: Sequence Alignment Pipeline
Full Description

NGSeasy : Sequence Alignment Pipeline


Next Generation Sequence Analysis Made Easy

A Dockerized and Virtulaized ngs pipeline and tool-box.

With NGSeasy you can now have full suite of NGS tools up and running on any high end workstation in an afternoon


The NGSeasy power tool

This is a large image (4.989 GB) containing all the tools needed to go from raw .fastq files to aligned .BAM to SNP and small INDEL variant calls .vcf .

As a multi-component system, NGS pipeline setup is traditionally heavy on configuration. Our idea is to provide this in a simple encapsulated container. Users also typically wish to configure their own environments and run the pipeline on a wide range of hardware (workstations to clusters to cloud), being able to stand-up a pipeline with minimal fuss is made straightforward with this container


Installed NGS tools

fastqc
trimmomatic
seqtk
fastx toolkit
bwa
bowtie2
stampy
novoalign (un-licensed)
GATK
picardtools
samtools
bedtools
bcftools
vcftools
playtpus
freebayes


NOTICE TO USERS OF THE CONTAINER IMAGE

While the software used to build the image is composed of free software versions some of the software has restrictions on use particularly for commercial purposes. Therefore if you wish to use this for commercial purposes, then you leagally have to approach the owners of the various components yourself!

This pipeline uses a number of pieces of software which require registration. By using this you are agreeing to observe the Terms and Conditions of the relevant pieces of software that compose this pipeline.

Software composing the pipeline requiring registration

If you want to build the image from the Dockerfile then you need to get your own versions of (below) in the build directory:

novoalign http://www.novocraft.com/
Stampy http://www.well.ox.ac.uk/project-stampy
GATK https://www.broadinstitute.org/gatk/

Docker Pull Command
Owner
compbio

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