Helpful software for bioinformatics

Here are some of the life savers that are not commonly introduced in standard bioinformatics curriculum. I think these toolkits encapsulate my understading of the spirit of programming: there must be an easier way to do it.

To Compare

directory and text files

Although unfavorable, sometimes it happens that one project directory is duplicated and the progress of analysis differs between each other. The tools that I have found to be very helpful for comparing different directories and files so that you can merge the two directory into one and keep the most updated files from each folder is Meld. I used to use WinMerge on Windows computer, too. But since Meld is available on both Ubuntu and Windows, I guess we can stick with that.

Meld is available on Ubuntu software


To just compare the pdf files, which I often need to because I read and annotate pdf both on my mobile device and computer, I use DiffPDF. I am not sure if Meld can handle pdf, but so far DiffPDF’s ability to compare all anotations is just great.

DiffPDF is available to download for Windows. Not sure about Ubuntu though, because I do not often use Ubuntu to read pdfs

To visualise


I do not know about you, but my brain is not powerful enough to automatically convert the fastq quality symbols to their ASCII number and calculate the quality score to provide me an overview of the base quality. Thus, I use fqless that converts the quality score to a colour, with intuitively green being good and red being bad, with different shades of orange in between.

fqless is available on GitHub

This post will be updated as I discover more software so stay tuned!

Timing Liu
Computational Biologist & Medical Student

Personalizing medicine