James Kane
@jameskane.blog
Software Engineer. Retro Computing. Genetic Genealogist. Fitness Enthusiast. TTRPG Gamer. Living the in the American Midwest.
Added 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-Elite
#genetic #genealogy #Big-Y #Y-Elite
August 15, 2026 at 9:10 PM
Added 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-Elite
#genetic #genealogy #Big-Y #Y-Elite
Starting 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.
decoding-us.org/ytree/node/R...
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.
decoding-us.org/ytree/node/R...
Ancestral origins · R-A9005 — Decoding Us
decoding-us.org
August 9, 2026 at 2:15 PM
Starting 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.
decoding-us.org/ytree/node/R...
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.
decoding-us.org/ytree/node/R...
The 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 #DataVisualization
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 #DataVisualization
August 6, 2026 at 12:15 PM
The 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 #DataVisualization
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 #DataVisualization
Added 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
There's a job setup to calculate new mutation rates when the sample size gets larger.
decoding-us.org/str-markers
#Genetic #Genealogy
Y-STR Markers — Decoding Us
decoding-us.org
July 29, 2026 at 1:06 PM
Added 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
There's a job setup to calculate new mutation rates when the sample size gets larger.
decoding-us.org/str-markers
#Genetic #Genealogy
Working 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.
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.
July 28, 2026 at 3:18 PM
Working 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.
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.
Latest 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 #Genealogy
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 #Genealogy
July 25, 2026 at 8:11 PM
Latest 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 #Genealogy
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 #Genealogy
🧬 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 👇
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 👇
July 12, 2026 at 2:53 PM
🧬 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 👇
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 👇
The 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.
July 4, 2026 at 6:05 PM
The 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.
OrangePi 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.
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.
![A Linux terminal window showing system information fetched via a neofetch-style tool. On the left is the Ubuntu logo in red ASCII art. On the right, the system specs read: jkane@CIX-Phecda-Board; OS: Ubuntu 26.04 LTS (Resolute R4); Host: CIX Phecda Board (1.0); Kernel: Linux 7.0.0-38-cix; Uptime: 3 mins; Shell: bash 5.3.9; DE: GNOME 50.1; WM: Mutter (Wayland); CPU: Cortex-A720*2 + Cortex-A520z; GPU: Mali-G720 MC10 [Integrated]; Memory: 5.54 GiB / 29.82 GiB. A row of color palette blocks sits at the bottom of the text.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:ppu2lhasfnyb4dkenakta4sp/bafkreiekz4yn33gnzgkgtzoux4w274koc5bezlqzyzoh4zeldtm4qgrhoa)
July 2, 2026 at 1:46 PM
OrangePi 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.
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.
I 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 #genealogy
#genetic #genealogy
June 18, 2026 at 7:38 PM
I 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 #genealogy
#genetic #genealogy
What 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)
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)
June 17, 2026 at 10:19 PM
What 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)
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)
First 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.
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.
June 17, 2026 at 8:19 PM
First 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.
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.
With 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.
June 15, 2026 at 12:56 PM
With 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.
The 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 #genealogy
June 15, 2026 at 11:02 AM
The 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 #genealogy
I 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 #genomics
June 9, 2026 at 5:57 PM
I 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 #genomics
My 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.
May 27, 2026 at 10:29 PM
My 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.
New blog entry up: jameskane.blog/2026/05/23/v...
Embedded Swift, Rust, and C++ have failed me for the last time. Time to write the compiler I want to use.
Embedded Swift, Rust, and C++ have failed me for the last time. Time to write the compiler I want to use.
Vestra: a systems language you can hold in your head
An introduction to Vestra, a Swift-flavored systems language whose grammar fits on two pages, and the v0 transpiler that lowers it to C++26.
jameskane.blog
May 23, 2026 at 2:21 PM
New blog entry up: jameskane.blog/2026/05/23/v...
Embedded Swift, Rust, and C++ have failed me for the last time. Time to write the compiler I want to use.
Embedded Swift, Rust, and C++ have failed me for the last time. Time to write the compiler I want to use.
Holy 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.
So tired of "winning." SBC's as a hobby are effectively dead in the current world.
May 22, 2026 at 4:25 PM
Holy 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.
So tired of "winning." SBC's as a hobby are effectively dead in the current world.
Working 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". hps://dl.acm.org/doi/10.1145/3577193.3593703
Early benches show 4x faster than bwa-mem2 with NEON patching with 1/3 RAM usage!
Early benches show 4x faster than bwa-mem2 with NEON patching with 1/3 RAM usage!
February 14, 2026 at 2:51 PM
Working 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". hps://dl.acm.org/doi/10.1145/3577193.3593703
Early benches show 4x faster than bwa-mem2 with NEON patching with 1/3 RAM usage!
Early benches show 4x faster than bwa-mem2 with NEON patching with 1/3 RAM usage!
After 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:
github.com/JamesKane/sw...
Expect changes as I find and fix the clanker's bugs and omissions.
github.com/JamesKane/sw...
Expect changes as I find and fix the clanker's bugs and omissions.
GitHub - JamesKane/swift-htslib: Swift bindings for HTSLIB
Swift bindings for HTSLIB. Contribute to JamesKane/swift-htslib development by creating an account on GitHub.
github.com
February 10, 2026 at 11:23 PM
After 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:
github.com/JamesKane/sw...
Expect changes as I find and fix the clanker's bugs and omissions.
github.com/JamesKane/sw...
Expect changes as I find and fix the clanker's bugs and omissions.
One 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.
February 6, 2026 at 2:13 AM
One 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.
Added 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.
github.com/JamesKane/bw...
Timings done with chm13v2.0 as the reference for 2,000,000 150 base pair reads on Apple Silicon.
github.com/JamesKane/bw...
Timings done with chm13v2.0 as the reference for 2,000,000 150 base pair reads on Apple Silicon.
February 5, 2026 at 3:51 PM
Added 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.
github.com/JamesKane/bw...
Timings done with chm13v2.0 as the reference for 2,000,000 150 base pair reads on Apple Silicon.
github.com/JamesKane/bw...
Timings done with chm13v2.0 as the reference for 2,000,000 150 base pair reads on Apple Silicon.
New 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.
January 20, 2026 at 7:25 PM
New 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.
Resurrecting 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.
December 22, 2025 at 11:06 PM
Resurrecting 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.