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Last pushed: 2 years ago
Short Description
NGSeasy Power Tool
Full Description

NGSeasy: Next Generation Sequencing Made Easy

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

Authors


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

Intsalled NGS tools


  1. fastqc
  2. trimmomatic
  3. seqtk
  4. fastx toolkit
  5. bwa
  6. bowtie2
  7. stampy
  8. novoalign (un-licensed)
  9. GATK
  10. picardtools
  11. samtools
  12. bedtools
  13. bcftools
  14. vcftools
  15. playtpus
  16. 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:

Docker Pull Command
Owner
snewhouse

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