Cade Mirchandani
@cademirch.bsky.social
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bioinformatics phd candidate @ ucsc
https://github.com/cademirch
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Cade Mirchandani
Ethan Linck
15 days 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...
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Cade Mirchandani
Bioinformatics Advances
19 days 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
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Dr. K. Lotterhos
18 days ago
New special issue in Molecular Ecology on Conservation Genomics
#popGen
#evolution
🧪🧬🖥️
onlinelibrary.wiley.com/toc/1365294x...
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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
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Cade Mirchandani
UC Santa Cruz Genomics Institute
21 days 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
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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
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Cade Mirchandani
Dmitri Petrov
20 days ago
What a beautiful paper!
www.nature.com/articles/s41...
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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
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Cade Mirchandani
Molecular Biology and Evolution
22 days 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
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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
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patak
about 1 month 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.
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Kendra "Gloom is My Beat" Pierre-Louis
about 2 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.
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Cade Mirchandani
Johannes Köster
3 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
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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
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Cade Mirchandani
Erik Enbody
3 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/...
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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
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Cade Mirchandani
Guido Meijer
3 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! 👇🧵
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Robert Aboukhalil
3 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.
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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
3 months ago
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Cade Mirchandani
Titus Brown
3 months ago
Preview of an important slide:
add a skeleton here at some point
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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
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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
4 months ago
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Cade Mirchandani
Matthew Feickert
4 months ago
Recording of the tutorial now up on the
@scipyconf.bsky.social
YouTube channel:
www.youtube.com/watch?v=8AYp...
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Arts, Feickert, & Kirkham - Reproducible Machine Learning Workflows for Scientists with pixi
YouTube video by SciPy
https://www.youtube.com/watch?v=8AYp3MlRSNA
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reposted by
Cade Mirchandani
6 months ago
Link to the new documentation pages: -
conda-forge.org/docs/mainta...
-
conda-forge.org/docs/mainta...
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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/
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Cade Mirchandani
Dax Kellie
6 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...
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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
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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
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7 months ago
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