Software Engineer. Retro Computing. Genetic Genealogist. Fitness Enthusiast. TTRPG Gamer. Living the in the American Midwest.https://bsky.app/profile/jameskane.bloghttps://bsky.app/profile/jameskane.blog/post/3mt5lirmqbk2bAdded a read remapping harness in Decoding-Us Navigator's latest Alpha build. Remap your hg37 or hg38 direct-2-consumer BAM to chm13v2.0 freely and locally on a computer with at least 16GB of RAM and a few hundred GB of disk space. #genetic #genealogy #Big-Y #Y-Elite15 Aug 2026 21:10 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mt5lirmqbk2bhttps://bsky.app/profile/jameskane.blog/post/3msnrjnjy7c2kStarting to work Block Tree aka Icicle tree rendering into decoding-us.org. Limiting these to the genealogical era as the amount of data blows up the further back you allow. ytree.net and FTDNA's render speeds are unacceptable. https://decoding-us.org/ytree/node/R-A9005/origins?level=country09 Aug 2026 14:15 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3msnrjnjy7c2khttps://bsky.app/profile/jameskane.blog/post/3msfzgaa5v222The latest feature branch for the Navigator project system is coming together: Icicle blocks derived from Alex Williamson’s ytree. Identification of shared SNPs, which may represent new branches. It should land in a new Alpha release this weekend. #YDNA #Genealogy #DataVisualization06 Aug 2026 12:15 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3msfzgaa5v222https://bsky.app/profile/jameskane.blog/post/3mrryjx3oxc2aAdded a new report at decoding-us.org, which displays the Y-DNA STR ranges, published mutation rates, and motif values where available. There's a job setup to calculate new mutation rates when the sample size gets larger. decoding-us.org/str-markers #Genetic #Genealogy https://decoding-us.org/str-markers29 Jul 2026 13:06 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mrryjx3oxc2ahttps://bsky.app/profile/jameskane.blog/post/3mrppgdfv3s2xWorking on an Archaic DNA module based on Altai, Chagyrskaya8, Denisova3 and Vindija33. Mostly working and Denisovan DNA being rejected for a European sample. Need to run on some Oceanic samples to validate the rest and clean-up the final reports.28 Jul 2026 15:18 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mrppgdfv3s2xhttps://bsky.app/profile/jameskane.blog/post/3mriof75pj22mLatest Alpha Build for Decoding-Us Navigator. Rewrote the Chromosome Painter to better isolate the two parents. Added more populations from public datasets. Fixed all the reported issues in older releases. #OpenSource #Genetic #Genealogy25 Jul 2026 20:10 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mriof75pj22mhttps://bsky.app/profile/jameskane.blog/post/3mqhgltdctc2m🧬 Introducing Navigator Alpha: a local desktop genomics app. Process BAM/CRAM, VCF, or chip tests (23andMe/Ancestry) offline with zero cloud uploads or privacy risks. Run Y/mt haplogroups, coverage, & ancestry on your own hardware. #Genomics #Bioinformatics #GeneticGenealogy 👇12 Jul 2026 14:53 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mqhgltdctc2mhttps://bsky.app/profile/jameskane.blog/post/3mptnjblxys26The Decoding-Us AppView is now running the Rust-version and hosting my latest chm13v2-based haplogroup trees. Y-DNA is sourced from IGSR samples and YDNA Warehouse samples. mtDNA is IGSR samples.04 Jul 2026 18:04 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mptnjblxys26https://bsky.app/profile/jameskane.blog/post/3mpo665vjw22kOrangePi 6 Plus running stock Ubuntu instead of the vendor image. Minimap2 alignment performance. Total Reads. Total Time Reads/Sec 615605482 3h 50m 0s 14ms 160592.571514783 Roughly the same performance as a 12-core Mac Pro 2013.02 Jul 2026 13:46 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mpo665vjw22khttps://bsky.app/profile/jameskane.blog/post/3mollcifmas23I am highly amused by Claude Code's thinking streams when dealing with FTDNA's Big Y VCF data. Everything I've muttered over the last decade when a BAM wasn't available, so I could just ignore their oddities. #genetic #genealogy18 Jun 2026 19:38 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mollcifmas23https://bsky.app/profile/jameskane.blog/post/3mojduny6ns2uWhat does a genotype-only pangenome callset miss, and what does it nail? I put numbers on both claims across chr20 & chr16, using 3 callers (vg, GATK, Delly) and a low-coverage PacBio HiFi long-read reality check. The trade-off is not what I expected. 🧵 (1/3)17 Jun 2026 22:19 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mojduny6ns2uhttps://bsky.app/profile/jameskane.blog/post/3moj54ekyc224First generation of the de novo mtDNA tree is live in the Decoding Us dev region. 🧬 Built using 1K Genomes raw data realigned to CHM13v2 (T2T), processed via GATK, and structured with IQ-TREE. Native, clean rendering of the U5a1 branch subclades. Moving beyond just Y-DNA.17 Jun 2026 20:18 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3moj54ekyc224https://bsky.app/profile/jameskane.blog/post/3mofmduj4ls2hTime to see how this #OrangePi 6 Plus handles minimap2. Initial impression is it's a loud boy with that stock fan.16 Jun 2026 10:40 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mofmduj4ls2hhttps://bsky.app/profile/jameskane.blog/post/3moddhohlnk2wWith the end of the Intel Mac era, I picked up a Late 2013 Mac Pro with dual AMD FirePro D700s. It's definitely a 13 year old machine, but still useful and an interesting desk ornament for the retro desk.15 Jun 2026 12:56 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3moddhohlnk2whttps://bsky.app/profile/jameskane.blog/post/3mod52cdm6k2jThe new Rust-base DecodingUs Navigator is coming along. Haplogroup detection and ancestry analysis working well. Still need to create the chm13v2 versions of a few panels. IBD via encrypted P2P between Navigators in progress. Then tidy up the consensus between multiple tests. #genetic #genealogy15 Jun 2026 11:01 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mod52cdm6k2jhttps://bsky.app/profile/jameskane.blog/post/3mnurhsiue222I tried to read my Y-DNA haplogroup straight out of a personal pangenome alignment. It confidently placed me in R1b, then steered me to the WRONG sub-branch. New post on what went wrong, and how I got the right answer. 🧬🌳 #bioinformatics #genomics09 Jun 2026 17:57 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mnurhsiue222https://bsky.app/profile/jameskane.blog/post/3mmukma2mzs2gMy SpaceMit K3 dev system arrived after some adventures with DHL. Performance is about 3x faster than the K1 on GeekBench 6. Firefly's AIBOX-K3 variant is nicely trimmed. Will run it as is for a bit before reimagine with a different OS.27 May 2026 22:29 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mmukma2mzs2ghttps://bsky.app/profile/jameskane.blog/post/3mmjnioo5c22fNew blog entry up: https://jameskane.blog/2026/05/23/vestra-a-systems-language-you-can-hold-in-your-head.html Embedded Swift, Rust, and C++ have failed me for the last time. Time to write the compiler I want to use.23 May 2026 14:21 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mmjnioo5c22fhttps://bsky.app/profile/jameskane.blog/post/3mmhdwswu7s2cHoly hell. My SpaceMit K3 board shipment was assessed nearly $150 in import fees to clear customs. So tired of "winning." SBC's as a hobby are effectively dead in the current world.22 May 2026 16:25 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mmhdwswu7s2chttps://bsky.app/profile/jameskane.blog/post/3metbgtdxj22jWorking on a rewrite of bwa-mem2 in #Swift 6 with a Metal acceleration path on Apple Silicon. Using the techniques from "Accelerating BWA-MEM Read Mapping on GPUs". hps://dl.acm.org/doi/10.1145/3577193.3593703 Early benches show 4x faster than bwa-mem2 with NEON patching with 1/3 RAM usage!14 Feb 2026 14:50 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3metbgtdxj22jhttps://bsky.app/profile/jameskane.blog/post/3mek473y4cs22After no success in finding a complete Swift binding for htslib for another project I've been planning, I had Claude whip one up. The code is reasonable so it's on Github: https://github.com/JamesKane/swift-htslib Expect changes as I find and fix the clanker's bugs and omissions.10 Feb 2026 23:23 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mek473y4cs22https://bsky.app/profile/jameskane.blog/post/3me5tew3v4c2sOne of these years I will not take a layoff from running for 2 months after race season, but this was not that year. 45 minutes of absolute destruction on the treadmill in the books.06 Feb 2026 02:13 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3me5tew3v4c2shttps://bsky.app/profile/jameskane.blog/post/3me4qmohrxk2gAdded a forked version of bwa-mem2 to my GitHub page, which compiles on ARM with NEON. Mostly leveraging sse2neon, but also some optimizations on top. https://github.com/JamesKane/bwa-mem2 Timings done with chm13v2.0 as the reference for 2,000,000 150 base pair reads on Apple Silicon.05 Feb 2026 15:51 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3me4qmohrxk2ghttps://bsky.app/profile/jameskane.blog/post/3mcuv4kpa2s2xNew SBC day. On paper the 32GB OrangePi 6 Plus should be pretty capable. I will need to setup and do some benchmarks after work tonight.20 Jan 2026 19:25 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mcuv4kpa2s2xhttps://bsky.app/profile/jameskane.blog/post/3mamdwd2h5k2nResurrecting an old project is always interesting to see how much your style and habits have evolved. Trying to get this minimal OS from the PowerPC era running on a RISC-V dev board is coming along. Almost enough POSIX here to attempt the Clang port.22 Dec 2025 23:06 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mamdwd2h5k2nhttps://bsky.app/profile/jameskane.blog/post/3mab6qansrc2lPlaying with a new UI in the Alpha version of the Navigator. We'll see if the analysis is able to pick-up that Illumina iSeq result is really an FGC Y Elite.18 Dec 2025 12:33 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mab6qansrc2lhttps://bsky.app/profile/jameskane.blog/post/3ma55x3su2c2aDeveloping a new Bulk Merge system for the #DecodingUs tree system. Tracks the source attributions in a hierarchy with a goal of replacement for the #ISOGG Y-DNA tree which is no longer being maintained. Working a few edge-cases on the forward-seeking in recursive descent and tree grafting.16 Dec 2025 22:09 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3ma55x3su2c2ahttps://bsky.app/profile/jameskane.blog/post/3m7on5lu3hc2wLast update to #DecodingUs for the year. Lot's of changes as I've rewritten all of the old site's systems on the new foundations. https://jameskane.blog/genomics/2025/12/10/DecodingUs-December-2025-Release.html Next up for 2026 is to work on the new Haplogroup Discover System. #genetic #genealogy11 Dec 2025 03:31 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m7on5lu3hc2whttps://bsky.app/profile/jameskane.blog/post/3m7kwlwkcn22kNew milestone for #DecodingUs. #ATProtocol identify login is complete, so I can use the Admin only tools for prelaunch stuff. More to follow when the Edge-compute companion is more than a buggy Alpha (also shown with some test data.)09 Dec 2025 16:09 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m7kwlwkcn22khttps://bsky.app/profile/jameskane.blog/post/3m7grwh6wts2mShipped new changes to the #DecodingUs App layer. Mostly small changes visible now: 1) Updated the FAQ. 2) Finally added a Search to the References/Papers in the curation portal. 3) Fixed a dumb bug when you share a link to a tree. Tons of enablers for connecting the Federation. decoding-us.com https://decoding-us.com08 Dec 2025 00:35 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m7grwh6wts2m