Bioinformatics in Graviton2 AWS
2
0
Entering edit mode
6 weeks ago
vm.higareda ▴ 20

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

genome assembly aws graviton2 • 360 views
ADD COMMENT
0
Entering edit mode
6 weeks ago

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.

ADD COMMENT
0
Entering edit mode
5 weeks ago
colindaven ★ 3.5k

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

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1612 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6