Excited to bump up TRUST4's version from 1.0.X to 1.1.0! We change the license from GPLv3 to MIT for more permissive use. Another feature is a huge speedup to data with barcode, e.g. single-cell data and TCR/BCR-seq with UMIs (--barcodeLevel molecule). github.com/liulab-dfci/TR…

Making Clair3-RNA available, which is a side project of my lab inspired by Fritz Sedlazeck and Miten Jain last December. It's for RNA long-read germline variant calling. It supports ONT r9 cDNA, ONT rna002 dRNA, PB Sequel2 Iso-Seq, PB Revio MAS-Seq. 🔗github.com/HKU-BAL/Clair3… 1/n

This is gem. Immediately sold when seeing Rule No 1 'The application is for the reviewer, not you, the applicant—remember that'. Elements of successful NIH grant applications | PNAS pnas.org/doi/10.1073/pn…

I've been updating my list of PacBio HiFi #metagenomics publications, and it looks like 2024 is off to a great start!

I count 9 published studies so far (pre-prints not included), but let me know if I missed any.

Here is a thread with the papers (alphabetical):
🧵 1/10

Our study evaluating the challenges of pan-genome analysis is now live on BioRxiv! biorxiv.org/cgi/content/sh… (1/17)

Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

The list of accepted short talks and posters (along with accepted papers) is now on our website! 🙌
recomb-seq.github.io/program/

Register today to join us in Boston on April 27-28!
recomb.org/recomb2024/reg…

🌟1/3: Introducing mm2-gb, GPU-accelerated Minimap2 for long-read DNA mapping!
🔥 mm2-gb accelerates Minimap2's bottleneck (chaining) on GPUs without compromising accuracy. 🚀 Kudos to Xueshen Liu Joy Dong, Satish Narayanasamy & Gina Sitaraman Computer Science and Engineering at Michigan AMD Michigan Engineering

Minipileup, a straightforward pileup-based multi-sample variant caller. Useful for data inspection or when mainstream callers are not applicable. Initially developed in 2012 as part of htsbox. Now released in a separate repo: github.com/lh3/minipileup

A blog post on the definition of pangenome: lh3.github.io/2024/03/29/wha…. In short:

* To microbiologists: a non-redundant set of genes
* More general: a collection of well assembled genomes

Join us in commemorating TB day 2024 by learning about drug resistant forms of the disease. In this detailed review we examine burden, gaps and innovations in care!

For the current (and future) users: AGC 3.1 (Assembled Genome Compressor) is ready for download: github.com/refresh-bio/agc
Main updates: support for ARM-based CPUs, e.g., Mac M1/M2/...; some bug fixes; some new features; speed optimizations.
Bioconda package should be ready soon.

Question: are there public human Nanopore RNA-seq data produced with SQK-PCS114 (cDNA-PCR Sequencing Kit V14)? Data from published papers would be preferred. Thanks!

Minimap2-2.27 introduces a new lr:hq preset (long read:high quality) for fast accurate mapping of Oxford Nanopore data.

The new preset is a huge ~4x reduction in CPU hours vs map-ont 🚀

Minimap2-2.27 released with new presets for accurate Nanopore reads and Illumina Complete Long Reads (both recommended by vendors), along with a few minor features and bug fixes. Output alignment identical to v2.26 except the value at a custom tag. github.com/lh3/minimap2/r…

If you have a Ph.D. in population genetics, computational biology, or bioinformatics and an interest in human health, you should come to Denmark for your postdoc and help us understand the role sex chromosomes play in autism. international.au.dk/about/profile/…

Congratulations to Peter Park member of the 2024 ISCB News Class of Fellows. Beyond all his well-known scientific achievements, Peter invested more than was asked for in teaching, in community support and mentorship. DBMI at Harvard Med is fortunate to have him as founder faculty.

What high-performance language to learn in bioinformatics? I have been asked many times on the question, so I decided to write down my thought in a blog post. This is going to be controversial.
lh3.github.io/2024/03/05/wha…