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Registration closed July 15.

BCC2020 is online, global, and affordable. The meeting and training are now done, and the CoFest is under way.

The 2020 Bioinformatics Community Conference brings together the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference into a single event featuring training, a meeting, and a CollaborationFest. Events run from July 17 through July 25, and is held in both the eastern and western hemispheres.

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Friday, July 17 • 21:01 - 23:30
Command Line Essentials for Bioinformaticians

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 Slides, TutorialVideo

This session is full.

We will start the session with a quick refresher on the basics of bash. I will then introduce a few well known unix tools and features of the shell with a focus on how to use these to make key bioinformatics tasks easier and more efficient.

Getting the most out of your shell (bash centric)
As bioinformaticians we regularly deal with directories filled with hundreds of files and have to manage running an equally large number of parallel jobs. There are many features of the shell that can make this easier. Here I will focus on some of the key ones that I use often.

Tools: bash (loops, functions, strings), xargs, parallel

Manipulating tabular data
Lots of bioinformatics data is tabular, gff, vcf, sam. Using these formats as examples I will introduce some useful tools for manipulating tabular data

Tools: cut, paste, awk, shuff, comm

Manipulating sequence data
Manipulating sequence data like fasta and fastq requires specialised bioinformatic tools. Two very useful ones are samtools and bioawk. This section will show you how to easily accomplish common tasks like splitting, sampling or reformatting a large sequence file.

Tools: samtools, bioawk

Prerequisites
  • A laptop with a modern web browser

Speakers
avatar for Ira Cooke

Ira Cooke

Senior Lecturer, James Cook University
Ira is interested in computational tools and workflows for analysing large ‘omics datasets. He applies these to a wide variety of research questions from clinical applications of genomics to human health to aquaculture and the biology of corals and cephalopods.His two main research... Read More →
WW

Wytamma Wirth

James Cook University
JZ

Jia Zhang

James Cook University
LF

Legana Fingerhut

James Cook University


Friday July 17, 2020 21:01 - 23:30 EDT
Training E