Bioinformatics in Graviton2 AWS

Question

[vm.higareda]

I am starting to explore amazon servicies to perform bioinformatics on illumina sequencing reads. Recently I read about Graviton2 which is based on ARM architecture. I am curious if the the most used software to perform genome assembly ie. spades or megahit could work on ARM architecture.

Any comments are welcome

Answer 1

[Alex Reynolds]

If source code is available, recompiling makes sense. The development kits are there.

There are some tips on compiling to ARM targets like the Graviton2 in this document:

https://aws.amazon.com/blogs/publicsector/generalized-approach-benchmarking-genomics-workloads-cloud-bwa-read-aligner-graviton2/

An idea is to replace calls to Intel SIMD intrinsics with ARM NEON calls, when compiling the relevant tools.

It's basically: edit, compile, benchmark.

Answer 2

[colindaven]

The conda people have been having a go, but it seems understandably like a work in progress:

https://github.com/conda/conda/issues/8297

[Alex Reynolds]

There's a link in there to Anaconda's support announcement: https://www.anaconda.com/blog/anaconda-aws-graviton2