Basic bioinformatics​ using command line

As sequencing technologies become more advanced and widespread, so does the need to be able to analyse the vast amount of data these technologies produce. There are numerous freely available online tools that can be used to analyse bacterial sequence data, many of which can be found as resources on the course pages for the Module 1 and 2 courses or is taught during those courses. However working and with and analysing genomic data using command line tools is a way to work faster, easier and more efficient by automating repetitive tasks and allows you to combine smaller tasks into more powerful workflows.

It can be very daunting to start down the path of bioinformatics using the command line without a strong background in computing and/or computer science. Here we have put together a list of introductory courses to command line which is already freely available online as well as a list of sites that offer in-person or online courses for a course fee and links to useful tools or guides.

Learning command line is like learning a new language and the learning curve can be steep. Do not be discouraged and remember "Google is your friend!". Whenever you encounter a problem, someone else has probably encountered it before and there can be great help in googling. 

This recent paper also provides ten simple rules that can help you when starting your command line journey:

Brandies and Hogg 2021 Ten simple rules for starting with command-line bioinformatics. PLOS Computational Biology

Freely available online courses​ and tutorials

Other courses

Some of the courses on these sites are freely available, others have participation fees.

  • NGS Academy for Africa CDC Pathogen Genomics initiative.
  • H3ABioNet - Provides courses on bioinformatics on a regular basis and has other resources available on their site

Tools and resources

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