Suggestions on Labtop Mac for Bioinformatics

Question

[joseph.landry]

Hi All,

I was wondering if someone could recommend a suitable Mac labtop computer that I could buy my graduate student to do standard bioinformatics / sequence analysis. The computer would be a Mac to allow the use of UNIX software. We would do RNA-Seq, ChIP-Seq, ATAC-Seq type analysis. We would have access to the university super computing cluster where we have the software to run alignments (Bowtie2, STAR, TopHat) and to store the large data sets and genome alignment files. The student would log into the cluster using the labtop to run the big jobs. Basically I would need him to have reasonable computing power to do secondary analysis once the peaks have been called and to do visualization (IGV and the like).

Can someone point me to a off the shelf system for him to use?

Best,

Joe

[Tota]

Also note that newer Apple laptops will move to ARM architecture, i.e. they'll no longer be running on Intel processors. Back when Macs moved from PowerPC to Intel there were a couple of issues, this was from what I've heard from peers.

Answer 1

[ATpoint]

I personally use a 2015 15'' Macbook Pro, i7 2.8Ghz Quad with 16Gb RAM and a 1TB SSD. Absolutely sufficient for any analysis I ran so far (ATAC, ChIP, RNA, scRNA-seq with up to 20k cells). I also outsource the hard work (alignment etc.) to a HPC. I like Mac over pure Linux as it still allows to use Microsoft Office natively which many of the coworkers use plus you don't have to compile every R package from source as on Ubuntu, not sure how this is with other Linux distros. Check the column on the right of this page for previous threads + the search function, this has been discussed many times before.

Answer 2

[MAPK]

I would buy Windows i7 laptops for less price. Recent Windows come with Windows Subsystem for Linux (WSL) or you can also install mobaxterm.

Answer 3

[Joe]

Really any Mac of the last few generations. I'd probably avoid the 2018 era ones as they had really shitty keyboards. I have a brand new 2020 13" i7 MacBook Pro and it does everything you'll ever need it to (SSH, MS Office etc).

That said, you don't need to spend anything like the amount of money Mac's demand for bioinformatics tasks.