It looks like we may be purchasing a new computer to run our newest sequencer (Oxford Nanopore MinION). We are looking at a desktop machine (not a cluster) that we can use both for running the MinION and for the downstream bioinformatics (e.g. samtools, bwa, canu, nanopolish). I am a wet labbie who has been given this task, so I am looking for an easy-to-use solution that will not break the bank. I would be very interested to hear any opinions regarding our options:
1. Apple Mac Pro ($$$ and less powerful than the rest)
2. Custom workstation running Windows 10 (Does the new Ubuntu bash work well enough? I have seen a lot of issues with Cygwin in my Googling)
3. Custom workstation running Ubuntu 14.0.4 (The sequencer software doesn’t seem to work well in Ubuntu)
4. Custom workstation with Windows 10/Ubuntu 14.0.4 dual boot (Was told this is not stable)
5. Custom workstation running Windows 10 and Ubuntu 14.0.4 virtually (Bioinformatics performance reduced?)
6. Custom workstation running Windows 10 and booting Ubuntu off of a USB (Bioinformatics performance reduced?)
7. Other options?
The Mac Pro seems most likely to work straight out of the box and give us the least headaches, but it is also much more expensive than comparable Windows/Linux boxes. It seems that the MinION software is developed for and works best under Windows, and from what I can tell, there have been issues with Linux. Has anyone used the new Bash shell integrated into Windows 10 to get some of the most standard bioinformatics programs running? Alternatively, does anyone have experience with how virtualization impacts bioinformatics performance?
Any input would be great. Thanks!
1. Apple Mac Pro ($$$ and less powerful than the rest)
2. Custom workstation running Windows 10 (Does the new Ubuntu bash work well enough? I have seen a lot of issues with Cygwin in my Googling)
3. Custom workstation running Ubuntu 14.0.4 (The sequencer software doesn’t seem to work well in Ubuntu)
4. Custom workstation with Windows 10/Ubuntu 14.0.4 dual boot (Was told this is not stable)
5. Custom workstation running Windows 10 and Ubuntu 14.0.4 virtually (Bioinformatics performance reduced?)
6. Custom workstation running Windows 10 and booting Ubuntu off of a USB (Bioinformatics performance reduced?)
7. Other options?
The Mac Pro seems most likely to work straight out of the box and give us the least headaches, but it is also much more expensive than comparable Windows/Linux boxes. It seems that the MinION software is developed for and works best under Windows, and from what I can tell, there have been issues with Linux. Has anyone used the new Bash shell integrated into Windows 10 to get some of the most standard bioinformatics programs running? Alternatively, does anyone have experience with how virtualization impacts bioinformatics performance?
Any input would be great. Thanks!
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