Free to read here: rdcu.be/dFqYo

We have released some raw Oxford Nanopore data for benchmarking purposes, along with some basecalled outputs.

We use the subset of 20k or 500k for benchmarking tools and methods a LOT!

We thought they would be helpful to others too.

4/5kHz R10.4.1 & RNA004

gentechgp.github.io/gtgseq/

Paraphase: a PacBio #bioinformatics tool for haplotyping segmental duplication genes. Applied to 160 locus, resolved copy numbers, de novo mutations, pseudogenes, low diversity gene example AMY1 as shown below.

biorxiv.org/content/10.110…

LongcallR is a SNP caller for long RNA-seq reads. It uses phasing to distinguish germline SNPs from A-to-I editing events which are frequent in RNA-seq data. It achieves decent SNP accuracy and reports the phasing of reads and SNPs. In Rust!

Excited to announce the release of longcallR, our small variant caller for long-read RNA-seq data! Big thanks to Heng Li. Also, catch my talk at RECOMBseq this Sunday April 28th at 1:50 pm. Can't wait to see you there! Github: github.com/huangnengCSU/l…

Q: I keep getting fast(er)q-dump timeout while our network looks ok. Does ncbi or sratoolkit implement a throttling mechanism? What is the solution?

Before you ask – fastq not available on ENA yet

A blog post on 'Where did BWA came from?': lh3.github.io/2024/04/12/whe…

Xiaowen's (Xiaowen Feng) new paper uses 16S in reads and k-mers to answer how much a metagenome assembly captures the species and sequence content in a sample. We found abundant species are not always assembled and proposed a heuristic to rescue some of them. genomebiology.biomedcentral.com/articles/10.11…

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