HAPHPIPE

How does HAPHPIPE compare to existing viral NGS pipelines and how was HAPHPIPE tested?

Please refer to our validation study.

NGS

What is the difference between next-generation sequencing and Sanger sequencing?

The critical difference between Sanger sequencing and NGS is sequencing volume. While the Sanger method only sequences a single DNA fragment at a time, NGS is massively parallel, sequencing millions of fragments simultaneously per run. This high-throughput process translates into sequencing hundreds to thousands of genes at one time. NGS also offers greater discovery power to detect novel or rare variants with deep sequencing.

I am new to using NGS data. Where should I start?

See this link for a beginner's guide to NGS analysis.

Using the Command Line

I am new to using the command line. Where should I start?

See this link for a beginner's guide to the command line.

What is a directory structure? Why is this important?

In computing, a directory structure is the way an operating system’s file system and its files are displayed to the user.

As researchers and software engineers, we should make sure that someone who is unfamiliar with our project is able to look at our computer files and understand in detail what we did and why.

We all have the rough experience where after a few months, we may simply not remember what we were up to when we created a particular set of files, or we may be forgetful about what conclusions were drew. We will either have to then spend time reconstructing previous experiments or lose whatever insights gained from those experiments.

So maintaining a well-structured directory is essential to both software development and bioinformatics.

What is an interactive job and how do I run one?

When using HAPHPIPE on an HPC cluster, if stages/pipelines are not being run in a job through SLURM or a similar package manager, HAPHPIPE commands should be run on an interactive node of your HPC. This guide gives instructions for using interactive nodes on GW's ColonialOne.

SRA

How do I download SRA files manually?

See the SRA search and download help site.

Conda

What is Conda?

See the Conda documentation here.

Bash

I am new to using bash. Where should I start?

See this link for a beginner's guide to bash scripting.