Pandagma: A tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole genome duplications academic.oup.com/bioinformati... 🧬🖥️ github.com/legumeinfo/p...

ColabPCR: A validated Google Colaboratory Notebook for Reproducible and Precise Primer Design. www.biorxiv.org/content/10.6... 🧬🖥️🧪 github.com/maurijlozano... colab.research.google.com/github/mauri...

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

Benchmarking of bioinformatics tools for the hybrid de novo assembly of human and non-human whole-genome sequencing data pubmed.ncbi.nlm.nih.gov/40703096/ 🧬🖥️🧪 github.com/genomicsITER...

Genome curation is the essential last step of genome assembly. It involves carefully stitching pieces of DNA together into chromosomes. This produces a genome assembly where each chromosome is represented by a single sequence - fulfilling the genome quality standard of @ebpgenome.bsky.social! (2/8)

🚨New paper published in @nature.com! Using pan-genetics across the Solanum genus🍅🥔🍆we reveal why gene duplications🧬are major contingencies in crop engineering. My postdoc work in the Lippman lab @CSHL, collab. with @katiejenike.bsky.social @mikeschatz.bsky.social chatz.bsky.social and many others!

GUIDE: Are you assembling a #genome for a polyploid? In this blog, Dr Camilla Ryan demonstrates how to go beyond the traditional collapsed genome and retain all haplotypes in the assembly. 🖥️ 🧬

Dot plots are an effective (if old school!) way to visualise the pairwise comparison of genomes.

For our recent pangenomics project (rdcu.be/d8PZ7), I wrote a small Python package to produce publication ready dot plots.

Check it out!

github.com/drboothtj/do...

pypi.org/project/dotp...

🧪🧬🦠

At least 15 Indigenous people in Arizona and New Mexico have reported being stopped at their homes and workplaces, questioned or detained by federal law enforcement and asked to produce proof of citizenship during immigration raids since Wednesday, according to Navajo Nation officials.

One of the cooler things I saw at the Nextflow summit a few months ago. Can't wait to try this.

New Article: "Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium" rdcu.be/d55Se

...chromosome-scale de novo assembled genomes of the representative accessions across 12 sections in Dendrobium, one of the largest orchid genera. #PlantScience

I love them. 🌸

My trip in Perú. 🌿⛰️