Computer specification for analysing NGS data

Question

[samakalyana.lvpei]

Hi, we are working on stool-metagenomics based on V3V4 and ITS2 amplicon sequencing. We would like to analyse data in a work station by using QIIME. Can someone help me with the best configuration (type of processor, RAM, hard disk storage) of work station that is required for analysing this NGS data (preferably for the data that is generated on an Illumina-MISeq platform; assuming for each sample nearly 2 GB of data is generated; and we need to analyse a maximum of about 120 such samples at a time).

[Sinji]

Do yourself a favor and spend that money on some AWS time. If you're looking to run 120 samples in parallel, then I can't really imagine a local machine being what you need.

[samakalyana.lvpei]

Hello Sinji, thankyou for your reply. 120 is the maximum number of samples we may need to analyse. But I need to know the hardware requirements to buy a work station, install QIIME in it and then do the analysis with samples ranging from 50 to 100 or 120 at a time. So, what configuration is optimum for such analysis?

Answer 1

[Kevin Blighe]

My own company's laptop, a 64-bit HP Pavilion 15 Notebook PC, has the following specs and has allowed me to perform 99% of bioinformatics analyses:

• 256kb L1 cache; 4MB L2 cache
• 16GB RAM
• 4 CPU cores (AMD A10-7300 Radeon R6, 10 Compute Cores 4C+6G)
• 2 TB hard-disk
• 3 x USB 2.0 ports (probably 1 of them is USB 3.0)

Now ~5 years old, it is charred on the underside from overheating in hot climates, the frame is warped, is missing 8 keys, and CD/DVD drive bay is 'broke'. Touchpad amazingly still works.

Disk is 75% full but I have archived another 1TB of data on online storage.

When I have needed to do something intensive, I rent Amazon resources.

Kevin