Which skills are most required to become a good bioinformatician?

Question

[m98]

I am half way through my PhD and I am considering pursuing a career in bioinformatics. My experience in bioinformatics is limited: I started coding 3 years ago but very slowly and my PhD is half bioinformatics half laboratory based. I currently have experience in bash and R. I am also trying to learn Python.

I am trying to find out how best to improve and prepare my CV for when I apply for jobs after my PhD. Any recommendations as to which skills in particular I should focus on would be greatly appreciated.

[Brian Bushnell]

Becoming adept in Python is very useful (one might say essential; you should be adept in some language (not R) and Python is a good choice). Becoming fluent with a wide variety of commonly-used bioinformatics software and data from different sequencing platforms is also a big plus. So, be able to take raw Illumina data and map it, call variants, look at the data in IGV; de-novo assemble the data and calculate coverage on the assembly; call peaks with Chip-SEQ; analyze differential expression with RNA-seq; taxonomically classify unknown contaminant reads; annotate variants with predicted effects of mutations on proteins; look for structural variations with long-read (PacBio/Nanopore) data; that sort of thing. It helps in interviews if you have personally done each of these on several different datasets so you know some of the nuances of them.

[ATpoint]

I agree that being able to use published tools, especially beyond!!! simply using the defaults is a big plus. A reasonable understanding of the theory behind the algorithms is also advisable to be able to adapt them to non-standard datasets. Still, I (also being a half-half student, far from being a proper programmer) prefer R much of Py or any other language, as Bioconductor offers a plethora of customizable packages that require a proper knowledge of R for efficient use. Beyond that, being able to write proper bash scripts to efficiently manipulate large files and automate repetitive tasks is a must. Experience in using a Linux cluster also helps, but that depends if your field requires large data handling.

[Ghoti]

Here are some resources I'm working through:

Bioinformatics tools/resources https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources

Online tutorial over bioinformatics which has a nice python section

Answer 1

[Bioaln]

This heavily depends on your field. I know bioinformaticians who more or less deal with webserver development, yet others mostly deal with low level algorithms, used by many others. R and py are definitely a plus, as prototyping becomes really, really fast.

Answer 2

[theobroma22]

Duplicate of Skills & qualities required to be a Bioinformatician

Answer 3

[m98]

Thanks to you all of you for your answers, that's really useful. Will definitely keep learning Python, R I know better but not in great depth (I still struggle while using specific rare packages). I also know Bash as I have to handle large datasets on the cluster. Thanks again!