Using shells other than bash As someone who's beginning to delve into bioinformatics, I'm noticing that like biology there are industry standards here, similar to Illumina in genomics and bowtie for alignment, many people use bash as shell. 

Is using a shell besides bash going to cause issues for me?
Bioinformatics tools written in shell and other shell scripts generally specify the shell they want to use (via #!/bin/sh or e.g. #!/bin/bash if it matters), so won't be affected by your choice of user shell.

If you are writing significant shell scripts yourself, there are reasons to do it in a Bourne-style shell.  See Csh Programming Considered Harmful and other essays/polemics.

A Bourne-style shell is pretty much the industry standard, and if you choose a substantially different shell you'll have to translate some of the documentation of your bioinformatics tools.  It's not uncommon to have things like


  Set some variables pointing at reference data and add the script to your PATH to run it:

export FOO_REF=/path/to/stuff
export PATH=/path/to/foo-x.y:$PATH
foo blah blah



These will typically be shown in Bourne-shell syntax.  By using a different shell you have to translate the export commands to your local syntax, and especially PATH munging is somewhat shell-dependent.

If you're experienced in Unix, this will be only a minor niggle.  If you're a beginner, IMHO this will add a non-negligible amount of friction on top of all the other things you're learning.