Compute resources

[KenSaville]

Hello Dr. Hamid

I'm thinking of using your book for teaching a bioinformatics class at ALbion College. Not until Fall 2026.

I was wondering what type of compute resources would be needed to get through the analyses / examples in the book. Is it something that would need a linux cluster or is it set up so it can be done on a decent laptop?

Thanks

K

[hamiddi]

Hi K — thanks for the thoughtful question!
I’ve just added a “Computational Resources & Hardware Requirements” section to the repository (see the README) that outlines both a teaching-friendly laptop setup and heavier options if you want to push full datasets.

Quick summary:
For course demos & exercises (recommended minimum):
4 cores, 16 GB RAM, 50–100 GB free disk

Linux or macOS preferred; Windows + WSL2 works well
Conda/Mamba environment with Python/R, Snakemake; Docker optional
Comfortable teaching workstation:
8+ cores, 32 GB RAM, 200–500 GB free disk
When a server/cluster helps (full datasets or longer labs):
RNA-Seq / Variant Calling: ~8–16 cores, 32–64 GB RAM, 200–500 GB scratch
ChIP-Seq: ~8–16 cores, 32–64 GB RAM, 200–400 GB
Genome Assembly (short reads): 16–32+ cores, 64–128 GB+ RAM, 0.5–2 TB
Shotgun Metagenomics: 16–32+ cores, 64–128 GB+ RAM, 1–3 TB
(We also provide downsampled teaching datasets so these run fine on laptops.)
No GPU is required for the book’s core workflows.

Thanks again—and excited you’re considering the book for Fall 2026!
Best regards;
Hamid

[hamiddi]

The issue has been resolved

…

On Mon, Nov 3, 2025 at 9:45 PM Ken Saville ***@***.***> wrote: *KenSaville* created an issue (hamiddi/ngs#2) <#2> Hello Dr. Hamid I'm thinking of using your book for teaching a bioinformatics class at ALbion College. Not until Fall 2026. I was wondering what type of compute resources would be needed to get through the analyses / examples in the book. Is it something that would need a linux cluster or is it set up so it can be done on a decent laptop? Thanks K — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A65IKBG2GFQONP5UGIC7CAD33AANJAVCNFSM6AAAAACLBS4AEGVHI2DSMVQWIX3LMV43ASLTON2WKOZTGU4DINBZGY4TMMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[KenSaville]

Sweet. Thanks for the quick reply. I am planning to use wsl. Will check to see if my set ups meet these requirements. Thanks again. K Ken Saville, PhD Professor Biology Department Albion College On Mon, Nov 3, 2025, 10:13 PM Hamid D. Ismail ***@***.***> wrote:

…

*hamiddi* left a comment (hamiddi/ngs#2) <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hamiddi_ngs_issues_2-23issuecomment-2D3483593284&d=DwMFaQ&c=t1KneP5CA95qj21Jnj2QJw&r=e3ZdNAYibFxoRcow6yQ3fREFMpFpV9Dd8c1m6OKS6uw&m=SWFMnLsn3B7BMHxCY3QW_VpsRA163botNB2FFaZ6trY8i6jVI_Isa9m4tKn67pyU&s=BEUUjT_qK8CZwN2ZtxqrFz51QeAMlmpUqk__jm-9iGc&e=> The issue has been resolved On Mon, Nov 3, 2025 at 9:45 PM Ken Saville ***@***.***> wrote: > *KenSaville* created an issue (hamiddi/ngs#2) > <#2 <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hamiddi_ngs_issues_2&d=DwQFaQ&c=t1KneP5CA95qj21Jnj2QJw&r=e3ZdNAYibFxoRcow6yQ3fREFMpFpV9Dd8c1m6OKS6uw&m=SWFMnLsn3B7BMHxCY3QW_VpsRA163botNB2FFaZ6trY8i6jVI_Isa9m4tKn67pyU&s=FoVLZvR1BFN2PDIBI3Zinlzj6s0ohycbcAG0RpYXkU4&e=>> > > Hello Dr. Hamid > > I'm thinking of using your book for teaching a bioinformatics class at > ALbion College. Not until Fall 2026. > > I was wondering what type of compute resources would be needed to get > through the analyses / examples in the book. Is it something that would > need a linux cluster or is it set up so it can be done on a decent laptop? > > Thanks > > K > > — > Reply to this email directly, view it on GitHub > <#2 <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hamiddi_ngs_issues_2&d=DwQFaQ&c=t1KneP5CA95qj21Jnj2QJw&r=e3ZdNAYibFxoRcow6yQ3fREFMpFpV9Dd8c1m6OKS6uw&m=SWFMnLsn3B7BMHxCY3QW_VpsRA163botNB2FFaZ6trY8i6jVI_Isa9m4tKn67pyU&s=FoVLZvR1BFN2PDIBI3Zinlzj6s0ohycbcAG0RpYXkU4&e=>>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/A65IKBG2GFQONP5UGIC7CAD33AANJAVCNFSM6AAAAACLBS4AEGVHI2DSMVQWIX3LMV43ASLTON2WKOZTGU4DINBZGY4TMMY <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_A65IKBG2GFQONP5UGIC7CAD33AANJAVCNFSM6AAAAACLBS4AEGVHI2DSMVQWIX3LMV43ASLTON2WKOZTGU4DINBZGY4TMMY&d=DwQFaQ&c=t1KneP5CA95qj21Jnj2QJw&r=e3ZdNAYibFxoRcow6yQ3fREFMpFpV9Dd8c1m6OKS6uw&m=SWFMnLsn3B7BMHxCY3QW_VpsRA163botNB2FFaZ6trY8i6jVI_Isa9m4tKn67pyU&s=IrMIxGbwMmKRxh-R-S3co_JiED10fWjFKjxEZsUrUQQ&e=>> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > — Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_hamiddi_ngs_issues_2-23issuecomment-2D3483593284&d=DwMFaQ&c=t1KneP5CA95qj21Jnj2QJw&r=e3ZdNAYibFxoRcow6yQ3fREFMpFpV9Dd8c1m6OKS6uw&m=SWFMnLsn3B7BMHxCY3QW_VpsRA163botNB2FFaZ6trY8i6jVI_Isa9m4tKn67pyU&s=BEUUjT_qK8CZwN2ZtxqrFz51QeAMlmpUqk__jm-9iGc&e=>, or unsubscribe <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AK6ZCVVF5JVNWUREIHOTH7333AKVLAVCNFSM6AAAAACLBS4AEGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTIOBTGU4TGMRYGQ&d=DwMFaQ&c=t1KneP5CA95qj21Jnj2QJw&r=e3ZdNAYibFxoRcow6yQ3fREFMpFpV9Dd8c1m6OKS6uw&m=SWFMnLsn3B7BMHxCY3QW_VpsRA163botNB2FFaZ6trY8i6jVI_Isa9m4tKn67pyU&s=TWmO4koMEN48ryO0uVwRIw4s96NUPzj7lrUjypLBp3g&e=> . You are receiving this because you authored the thread.Message ID: ***@***.***>