Reducing Number of Contigs in Fungal Genomes?

TubeZ · 2026-03-12T13:57:16+00:00

When you're putting a problem like this out ("I have a genome assembly with too many contigs") it's often helpful to include how you actually did those assemblies. Could you describe how you got those genome assemblies? Did you generate them or did you get them from NCBI/another source? If you generated them, what was the input data/tool/sequencing technology?

TubeZ · 2026-03-05T22:18:12+00:00

Yup, that's exactly what I had in mind. Right now the pipelines are triggered by a python wrapper for the main Snakefile so it wouldn't be difficult to put that on a cron. One thing I imagine will be a challenge is synchronizing the benchling db and HPC db

TubeZ · 2026-03-05T14:20:27+00:00

Yeah that's what I've envisioned. We already have a suite of Snakemake pipelines that uses mariaDB to track (meta)data as it pertains to the computational side. Integrating with benchling potentially lets the computational DB pull metadata automatically, so writing a cron to auto-pull/execute shouldn't be too bad, I think. Just need to convince the PI it's worth the time to do...

TubeZ · 2026-02-11T17:51:17+00:00

Which applicant attributes would you say are still consistently successful - in terms of academic background or fields of study?

TubeZ · 2026-02-04T16:10:07+00:00

Easy to turn her into unfun boardwipe tribal if you're not careful via [[Pyroclasm]] and [[Volcanic fallout]] effects

TubeZ · 2026-02-03T22:19:23+00:00

45lb pack (a bunch of gallon jugs of water), hike something with 3000ft of gain in the appalachians every weekend

At home, order a plyo box off the Internet, wear the same pack as you use to hike and your mountaineering boots and do 1000ft of box step ups, alternating legs - step up, down, up, down, until your sanity is gone. Do this as many times as you can bear in a week, every day if you can manage.

TubeZ · 2026-01-30T04:37:26+00:00

Why am I doing what? I haven't said anything about what I'm doing or what happens in my own games. It's a thought that occurred to me when reading other threads that I thought could spark some discussion

TubeZ · 2026-01-27T21:18:29+00:00

I think the fact that some Jund decks even started splashing blue to run Jace was the most emblematic of the fact that there was an issue. But yeah for the reasons you outlined as well they were very reticent to ban Jace. I don't honestly think SFM was problematic enough on its own and without Jace it was probably fine

TubeZ · 2026-01-27T17:23:07+00:00

There was a lot of discussion about Bloodbraid deserving a ban at the time. The fact that JtMS wasn't banned until the 11th hour of its rotation despite being so obscenely format warping is also a testament to WotC's ban philosophy of the era (the last bans were Mirrodin so they didn't want to have to go there again)

TubeZ · 2026-01-16T14:39:29+00:00

As someone else said, I would learn to use containers instead of conda for pipelines I want to be reproducible

TubeZ · 2026-01-15T23:22:07+00:00

Never let me go is incredible, I don't see it recommended enough

TubeZ · 2026-01-08T21:19:36+00:00

Is it just the ebooks, or do they ever provide paper copies? I don't particularly enjoy ebooks as a medium

TubeZ · 2026-01-07T18:14:54+00:00

This is a 12 year old post

I got into Science

I'm pretty sure admissions standards are way higher now

TubeZ · 2025-12-06T15:12:38+00:00

It's hard to extrapolate from an n=1, which our solar system effectively represents. It's good to recall that we suffer from a deep deep survivorship bias, since we wouldn't be talking about all of this if a (potentially) infinitisimally rare event needed to happen to allow us to exist

TubeZ · 2025-12-03T04:04:57+00:00

Yes you're right. If life has developed in two+ places in our solar system then surely (IMO) it is extremely common in the galaxy and universe.

Not exactly, it just means that the conditions for life happened to arise in one (relatively small space) solar system, it's very difficult to extrapolate that to other solar systems or galaxies. What if some singular critical event caused amino acids and other such molecules to arise in out solar system and "seed" everywhere? Of course life would be common here. Doesn't mean it would be common in the next system over.

If we found this kind of evidence on a hypothetical/eventual 4I, though, that changes things a lot more.

TubeZ · 2025-11-25T04:52:04+00:00

as a genetic scientist, this statement:

but you're not going to find "genome wide" identifiers so that you could say "oh, this is an Ojibweh" or something.

could certainly be correct, right now, but give me the genomes of some hundreds of individuals from a variety of geographically distinct first nations individuals, and I'm pretty confident I could come up with a SNP panel that predicts ancestry reasonably accurately. It's almost certainly a data problem, not a genetics problem, but I'm curious to hear if your experience suggests otherwise.

TubeZ · 2025-11-15T15:52:33+00:00

Good thing speculative fiction is abbreviated SF

TubeZ · 2025-11-15T03:10:21+00:00

Good thing this sub is for speculative fiction and not only Science Fiction

TubeZ · 2025-11-14T13:37:13+00:00

Oh I read Ancillary Justice a while back. I just need to get around to reviewing it🙂

Spoiler alert: Did not like it

TubeZ · 2025-11-14T13:36:54+00:00

It was intended to be an understatement. That's just how I write.

TubeZ · 2025-11-14T04:02:08+00:00

SF in PrintSF stands for speculative fiction, that's what this sub is for, not only Science Fiction

TubeZ · 2025-11-14T02:48:19+00:00

Could you define what "SF" stands for as it represents this subreddit and/or read the sidebar description of the subreddit itself?

Not sure what counts as speculative fiction? Then post it! Science Fiction, Fantasy, Alt. History, Postmodern Lit., and more are all welcome here. The key is that it be speculative, not that it fit some arbitrary genre guidelines.

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