don't use hg38.fa as-is. checkout the references 😜 here: ftp-trace.ncbi.nlm.nih.gov/ReferenceSampl… rendered the ipynb (not mine) here: gist.github.com/brentp/1935e9b… in short, use: GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta.gz other updates on the best hg38 reference?

Our #DRAGEN methods paper in Nature is out. Proud of team Illumina and the collaboration with Fritz Sedlazeck BCM HGSC! Learn about the accuracy, scalability, the multi-genome mapping, machine learning, callers for genes in difficult to map regions. nature.com/articles/s4158…

#DRAGEN Illumina method fully described & benchmarked out in Nature Biotechnology: nature.com/articles/s4158… Graph genome based detection of SNV, STR, SV, CNV all in 30 min! Improvements in all variants! Huge thanks to Severine Catreux Rami mehio Sairam Behera BCM HGSC #Bioinformatics 1/5

#DRAGEN is now out in Nature Biotechnology . We outline the method, which has been benchmarked and also analyzed using the 1KGP cohort. It demonstrates accuracy and scalability through graph genome and machine learning approaches. nature.com/articles/s4158…

Comprehensive genome analysis and variant detection at scale using DRAGEN go.nature.com/4eXQRT1

New in Nature Biotechnology: Illumina #DRAGEN marks milestone in sequencing data analysis, enabling insights across various diseases with a highly comprehensive, scalable #bioinformatics platform. Sairam Behera Severine Catreux Rami mehio Fritz Sedlazeck nature.com/articles/s4158…

K-mer analysis of long-read alignment pileups for structural variant genotyping. #Kmers #LongReads #AlignmentPileup #StructuralVariants Fritz Sedlazeck bioRxiv biorxiv.org/content/10.110…

Fritz Sedlazeck Rami mehio Severine Catreux Sairam Behera BCM HGSC Illumina BCM Department of Molecular and Human Genetics BCMHouston Rice Computer Science Validation testing of next-gen genome analysis platform reveals potentially disruptive tech #NBTintheNews via Phys.org phys.org/news/2024-11-v…

Luis Paulin on detection of mosaics structural variation with Sniffles2 #ASHG24

The Long-read sequencing Special Issue is now LIVE! Guest-edited by Alexander Hoischen, Fritz Sedlazeck, and AnaConesa!

Our first curated draft somatic structural variant benchmark for the new GIAB PDAC tumor cell line HG008-T is at ftp-trace.ncbi.nlm.nih.gov/ReferenceSampl…, based on extensive short+long read sequencing data described in doi.org/10.1101/2024.0…. Feedback to improve future versions is very welcome!

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS, indeterminate dendritic cell histiocytosis

The new issue of Genome Research is now live! Follow the link to new research on mitochondrial–nuclear gene expression regulation, guppy Y Chromosome genomics, and more! tinyurl.com/Genome-Res-35-3

We summarized state-of-the-art computational methods for DNA methylation analysis using long-read sequencing, covering everything from base calling to sample-level, cell-type-level, and even population-scale analysis. Huge Thanks to Fritz Sedlazeck and Winston Timp for this great work!