Cade Mirchandani
@cademirch.bsky.social
📤 57
📥 105
📝 17
bioinformatics phd candidate @ ucsc
https://github.com/cademirch
reposted by
Cade Mirchandani
BF Francis Ouellette
about 15 hours ago
From
@davidmoreau.bsky.social
& Kristina Wiebels in
@plos.org
#Computational
#Biology
| Nine quick tips for
#software
#containerization
| I like all Tips, but particularly Tip 9: Plan for sharing & longevity |
#Bioinformatics
#Education
#PLOSCBQT
| 🧬 🖥️ 🧪 🔓 ⬇️
journals.plos.org/ploscompbiol...
loading . . .
Nine quick tips for software containerization
Software containerization has become a cornerstone of modern computational biology, enabling researchers to package code, dependencies, and execution environments in portable and reusable units. Conta...
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014197
0
1
1
reposted by
Cade Mirchandani
BF Francis Ouellette
22 days ago
From
@robert.bio
@helenechiapello.bsky.social
@mthomaschollier.bsky.social
& col. in
@plos.org
#Computational
#Biology
| Training biologists in
#Unix
command-line skills: From curriculum to interactive online tutorials|#Education
#OpenEducationalResources
| 🖥️ 🧪 ⬇️
journals.plos.org/ploscompbiol...
loading . . .
Training biologists in Unix command-line skills: From curriculum to interactive online tutorials
As the generation of data in the life and health sciences expands rapidly, there is a growing need for professionals and students in these fields to master core bioinformatics skills, particularly tho...
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014133
1
15
8
reposted by
Cade Mirchandani
Brant Faircloth
22 days ago
In about an hour using Claude Code (see disclaimer in repo) I put together code to do something that is a pain in the ass to do manually - find a good genome in NCBI then see what decent population level WGS data exist for that genome assembly in NCBI SRA:
github.com/brantfairclo...
. I'm impressed.
loading . . .
GitHub - brantfaircloth/pop-genome-checker
Contribute to brantfaircloth/pop-genome-checker development by creating an account on GitHub.
https://github.com/brantfaircloth/pop-genome-checker
2
8
2
reposted by
Cade Mirchandani
rOpenSci
24 days ago
[blog] A Better R Programming Experience Thanks to Tree-sitter Did you know how Tree-sitter's support for R help you get ✨ reformatting through Air and linting through Jarl; ✨ auto-completion or help on hover in the Positron IDE; ✨ better search for R on GitHub; ✨ and more! By
@maelle
[…]
loading . . .
Original post on hachyderm.io
https://hachyderm.io/@rOpenSci/116334769160060733
0
4
3
reposted by
Cade Mirchandani
bioRxiv Bioinfo
26 days ago
Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes
https://www.biorxiv.org/content/10.64898/2026.03.29.711974v1
0
4
2
reposted by
Cade Mirchandani
Christian Meesters
27 days ago
The
#snakemakehackathon2026
has ended, we are still preparing our preprint release. But, our host has prepared a note on their homepage: https://go.tum.de/946236 🥳
#snakemake
#reproduciblecomputing
loading . . .
Snakemake Hackathon 2026 – faster and further improved reproducible data analysis
Snakemake Hackathon 2026 delivers even faster and further improved support for reproducible data analysis. The 2026 Snakemake Hackathon brought together about 40 experts in Munich to deliver major improvements, new features, and performance enhancements for reproducible data analysis. Their community driven work strengthens Snakemake’s scalability, usability, and support for modern scientific workflows.
https://www.mdsi.tum.de/en/mdsi/latest-info/news/full-text/article/snakemake-hackathon2026-faster-and-further-improved-reproducible-data-analysis/
0
3
1
reposted by
Cade Mirchandani
Aaron Quinlan (he/him)
about 1 month ago
We've launched a department Trainee Emergency Fund, to help support EVERYONE BELONGING IN SCIENCE by meeting urgent financial needs of students and postdocs. Click to learn more about our goal with this fund and to donate!
www.givecampus.com/schools/Univ...
loading . . .
LinkedIn
This link will take you to a page that’s not on LinkedIn
https://lnkd.in/gF53G-UF
0
10
7
reposted by
Cade Mirchandani
Michael Hall
about 1 month ago
🐍 For all ye
#snakemake
users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳 The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.). See
github.com/snakemake/sn...
for more
loading . . .
GitHub - snakemake/snakefmt: The uncompromising Snakemake code formatter
The uncompromising Snakemake code formatter. Contribute to snakemake/snakefmt development by creating an account on GitHub.
https://github.com/snakemake/snakefmt
0
18
7
reposted by
Cade Mirchandani
Johannes Köster
about 1 month ago
Another terminal based tool to interactively monitor all running
#Snakemake
workflows is
#snkmt
:
github.com/cademirch/sn...
.
loading . . .
GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.
A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt
https://github.com/cademirch/snkmt
1
10
4
reposted by
Cade Mirchandani
Wytamma
about 1 month ago
At the
#SnakemakeHackathon2026
in Munich last week I complied Snakemake to
#Wasm
and made a client-side webapp for creating and sharing workflows ->
snakemake.github.io/snakemake-wa...
. It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
add a skeleton here at some point
0
12
5
reposted by
Cade Mirchandani
Chris Smith
about 1 month ago
I'm hiring a postdoc in population and evolutionary genetics at Indiana University Bloomington! Computational lab. Message me if interested, and can apply here:
indiana.peopleadmin.com/postings/32547
loading . . .
Postdoctoral Fellow, Biology
The department of Biology is a large, unified department with strong undergraduate degrees, nationally-ranked graduate programs, and world-class research spanning the breadth of biological questions a...
https://indiana.peopleadmin.com/postings/32547
0
10
16
reposted by
Cade Mirchandani
Robert McNees
about 2 months ago
There's a "is anyone even reading this" sort of honesty you get in the software update release notes from a project that's been around for a long time.
19
1337
346
reposted by
Cade Mirchandani
Daniel Abraham
about 2 months ago
Came across the phrase "cognitive DDOS" to describe our present culture. Understood instantly what it meant.
10
2756
1019
reposted by
Cade Mirchandani
Rob Patro
2 months ago
I’ve written a post about my recent experiences (successes) with AI coding models; the experiences that caused me to re-evaluate my initial judgements, the surprise I had at what can be accomplished, & some fears I have about these tools. Discussion welcome!
combine-lab.github.io/blog/2026/02...
loading . . .
COMBINE-lab - The skeptic’s guide to generative AI assisted coding
An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more.
https://combine-lab.github.io/blog/2026/02/15/a-skeptics-guide-to-generative-ai-coding.html
8
52
20
reposted by
Cade Mirchandani
Graham Coop
2 months ago
Excited for this. Teaching popgen is one of my favourite parts of my job and I've wondered about doing an online version of the class for sometime. Teaming up with
@jrossibarra.bsky.social
to do this is wonderful.
add a skeleton here at some point
2
42
20
reposted by
Cade Mirchandani
Jeffrey Ross-Ibarra
3 months ago
Playing with
sandbox.bio
. This was remarkably cathartic.
1
14
3
reposted by
Cade Mirchandani
David Asboth
3 months ago
A succinct and useful list of rules for teaching data science, including some of my favourites: "teach with real data" and "have students do projects".
#databs
#datasky
add a skeleton here at some point
1
15
2
reposted by
Cade Mirchandani
Johannes Köster
3 months ago
I've just released
#rust-htslib
1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling.
github.com/rust-bio/rus...
1
17
7
reposted by
Cade Mirchandani
Richard Lenski
3 months ago
Looking for something new to integrate into an
#evolution
or
#microbiology
course? Useful for lectures, labs, homework? Have a look at our STEPS program, which simulates bacterial evolution, including the
#LTEE
. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.
add a skeleton here at some point
1
78
55
reposted by
Cade Mirchandani
Ragnar {Groot Koerkamp}
3 months ago
vibe coding is the new doom scrolling?
add a skeleton here at some point
1
3
2
reposted by
Cade Mirchandani
Sina Majidian
3 months ago
Super-pangenome analyses across 35 accessions of 23 Avena species highlight their complex evolutionary history and extensive genomic diversity
doi.org/10.1038/s415...
Common oat=Avena sativa
0
9
2
reposted by
Cade Mirchandani
Titus Brown
3 months ago
Once more unto the breach: A fast introduction to snakemake, in 5 examples.
loading . . .
A fast introduction to snakemake (in 5 examples) - HackMD
# A rapid introduction to snakemake (in 5 examples) See github repo: [ctb/2026-rapid-snakemake-intr
https://hackmd.io/@ctb/Bk_0aXrHWl#/
0
11
4
reposted by
Cade Mirchandani
Felix Wiegand
4 months ago
🚀 Our new paper on Alignoth just published in Bioinformatics! Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows. 📄
doi.org/10.1093/bioi...
#bioinformatics
#genomics
#rust
@johanneskoester.bsky.social
1
21
10
reposted by
Cade Mirchandani
Tristan A.F. Long
4 months ago
With population genetics on deck for
#BI111
this week, preparations for HWE exercises for 1100+!students means lots of card-sorting!
add a skeleton here at some point
2
12
6
reposted by
Cade Mirchandani
Ethan Linck
4 months ago
I've slowly been reformatting notes from my population and conservation genetics course at Montana State University into a web book—a rough draft is now live here:
elinck.org/popgen_conge...
1
133
61
reposted by
Cade Mirchandani
Bioinformatics Advances
4 months ago
🧬 Just out in Bioinformatics Advances: “tskit arg visualizer: Interactive plotting of ancestral recombination graphs.” Read the full paper here: https://doi.org/10.1093/bioadv/vbaf302 Authors include:
@kitchensjn.bsky.social
,
@yanwong.bsky.social
1
18
13
reposted by
Cade Mirchandani
Dr. K. Lotterhos
4 months ago
New special issue in Molecular Ecology on Conservation Genomics
#popGen
#evolution
🧪🧬🖥️
onlinelibrary.wiley.com/toc/1365294x...
loading . . .
Special Issue: CONSERVATION GENOMICS ‐ MAKING A DIFFERENCE: Molecular Ecology: Vol 34, No 23
Molecular Ecology is an international journal for research using molecular genetic techniques to address questions in ecology, evolution, behavior and conservation.
https://onlinelibrary.wiley.com/toc/1365294x/2025/34/23?campaign=woletoc
0
44
26
reposted by
Cade Mirchandani
UC Santa Cruz Genomics Institute
4 months ago
Announcing bamdam: a new open source tool for studying ancient DNA 🧬 It shrinks massive metagenomic files by 10x and helps distinguish ancient sequences from contamination. Tested on the oldest DNA yet uncovered (2M years)
link.springer.com/article/10.1...
@bdesan.bsky.social
@russcd.bsky.social
loading . . .
Bamdam: a post-mapping authentication toolkit for ancient metagenomics - Genome Biology
Ancient metagenomic studies using capture or shotgun sequencing often perform pairwise alignment of individual reads against large reference databases followed by lowest common ancestor assignment for...
https://link.springer.com/article/10.1186/s13059-025-03879-x
0
9
6
reposted by
Cade Mirchandani
Dmitri Petrov
4 months ago
What a beautiful paper!
www.nature.com/articles/s41...
loading . . .
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
https://www.nature.com/articles/s41586-025-09798-y
1
41
8
reposted by
Cade Mirchandani
Molecular Biology and Evolution
4 months ago
@cademirch.bsky.social
@erikenbody.bsky.social
TB Sackton &
@russcd.bsky.social
introduce Callable Loci And More (clam), a tool that leverages callable loci to accurately estimate population genetic statistics (π, dxy, and FST). 🔗
doi.org/10.1093/molbev/msaf282
#evobio
#molbio
#compbio
loading . . .
Efficient Estimation of Nucleotide Diversity and Divergence Using Callable Loci (and More)
Abstract. The increasing scale of population genomic datasets presents computational challenges in estimating summary statistics such as nucleotide diversi
https://doi.org/10.1093/molbev/msaf282
0
20
14
reposted by
Cade Mirchandani
patak
5 months ago
The changed code is a small fraction of an open source contribution. Your commitment to understand the issue, how your proposed solution fits with the project, and be ready to own and push the review process forward is the biggest chunk of the work. Your effort is the contribution, not the code.
5
448
72
reposted by
Cade Mirchandani
Kendra "Gloom is My Beat" Pierre-Louis
6 months ago
Friendly reminder that dishwashers made after 1995 or so are so water and energy efficient that even if you ran them twice fully loaded it would still use less water than handwashing the same load. So many "green" things feel like sacrifices. Dishwashers are not one of them.
86
4651
1102
reposted by
Cade Mirchandani
Johannes Köster
6 months ago
Want to help shaping the future of
#Snakemake
? Then participate in the Snakemake hackathon 2026 in Munich! There's still room as the maximum number of participants is not yet reached. You can register here:
indico.cern.ch/e/snakemake-...
#sciworkflows
#reproducibility
loading . . .
Snakemake Hackathon March 2026
We are excited to announce the Snakemake Hackathon 2026, to be held 9-13 March, 2026 at the Technical University Munich. This event will bring together passionate developers and data scientists to col...
https://indico.cern.ch/e/snakemake-meeting-2026
0
5
5
reposted by
Cade Mirchandani
Erik Enbody
6 months ago
Check out the latest paper from the CCGP on California Quail and the ecological and anthropogenic factors that impact genomic variation. Led by Phred Benham and the Bowie group:
onlinelibrary.wiley.com/doi/10.1111/...
loading . . .
Patterns of Genetic Diversity Within Three California Quail Species Are Best Explained by Climate and Landscape Changes
Many North American game animals experienced severe population declines during the 19th century due to market hunting. However, estimates of the timing and magnitude of these declines often rely on a...
https://onlinelibrary.wiley.com/doi/10.1111/mec.70093
0
7
4
reposted by
Cade Mirchandani
Guido Meijer
6 months ago
Want to make publication-ready figures come straight from Python without having to do any manual editing? Are you fed up with axes labels being unreadable during your presentations? Follow this short tutorial including code examples! 👇🧵
2
158
50
reposted by
Cade Mirchandani
Robert Aboukhalil
7 months ago
Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa:
sandbox.bio/concepts/bwt
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
loading . . .
3
99
31
Monthly Snakemake developer meeting: Tuesday, Sept 30th at 6am PST! Open to all - developers & users. We discuss issues/PRs and cowork on Snakemake projects. DM me to join!
#snakemake
#workflows
#opensource
#bioinformatics
#oss
7 months ago
1
5
0
reposted by
Cade Mirchandani
Titus Brown
7 months ago
Preview of an important slide:
add a skeleton here at some point
1
7
1
snkmt 0.2.0 is out! New features: 1. Multi-database support - switch between dbs via ctrl+p (like VSCode) 2. Workflow filtering - hide/filter by snakefile, status, or date for cleaner navigation
github.com/cademirch/sn...
#snakemake
#bioinformatics
#workflow
#opensource
#python
#cli
#tui
loading . . .
GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.
A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt
https://github.com/cademirch/snkmt
7 months ago
0
6
2
reposted by
Cade Mirchandani
Matthew Feickert
8 months ago
Recording of the tutorial now up on the
@scipyconf.bsky.social
YouTube channel:
www.youtube.com/watch?v=8AYp...
loading . . .
Arts, Feickert, & Kirkham - Reproducible Machine Learning Workflows for Scientists with pixi
YouTube video by SciPy
https://www.youtube.com/watch?v=8AYp3MlRSNA
0
4
3
reposted by
Cade Mirchandani
Prefix.dev - the Pixi company
10 months ago
Link to the new documentation pages: -
conda-forge.org/docs/mainta...
-
conda-forge.org/docs/mainta...
loading . . .
Rust packages | conda-forge | community-driven packaging for conda
If you want to package a Rust package to conda-forge, you can use this recipe template:
https://conda-forge.org/docs/maintainer/example_recipes/rust/
0
2
1
reposted by
Cade Mirchandani
Dax Kellie
10 months ago
Some great tips on making better
#dataviz
👇 In my experience, the final point—feedback—is invaluable Funny how another person might focus on something completely different to what you intended 🙃 Adjusting from this feedback always makes for a clearer visual message📊🧪
www.nature.com/articles/s41...
loading . . .
A checklist for designing and improving the visualization of scientific data - Nature Cell Biology
Creating clear and engaging scientific figures is crucial to communicate complex data. In this Comment, I condense principles from design, visual perception and data visualization research in a checkl...
https://www.nature.com/articles/s41556-025-01684-z
1
16
7
Excited to share the
#Snakemake
monitoring tool I've been working on: snkmt (Snakemate) - a CLI utility for real-time workflow monitoring. Basically solves the "is my pipeline still running?" problem and makes debugging failed jobs much easier.
#bioinformatics
#workflow
#opensource
1/3
11 months ago
1
13
4
you reached the end!!
feeds!
log in