James Kane
@jameskane.blog
Software Engineer. Retro Computing. Genetic Genealogist. Fitness Enthusiast. TTRPG Gamer. Living the in the American Midwest.
The latest installers can be found at decoding-us.org/download.
3-Clause BSD source code: github.com/JamesKane/de...
3-Clause BSD source code: github.com/JamesKane/de...
Download the Navigator — Decoding Us
decoding-us.org
August 15, 2026 at 9:10 PM
The latest installers can be found at decoding-us.org/download.
3-Clause BSD source code: github.com/JamesKane/de...
3-Clause BSD source code: github.com/JamesKane/de...
MDKA informational boxes for samples under the terminal branches for people who opt-in from Navigator is the current work in progress.
August 9, 2026 at 2:17 PM
MDKA informational boxes for samples under the terminal branches for people who opt-in from Navigator is the current work in progress.
Built in Rust with no complex dependencies, Navigator supports "progressive consensus" to cross-check multiple DNA kits & syncs anonymized results via AT Protocol for tree building.
Join the Alpha: jameskane.blog/genomics/202...
#RustLang #ATProto #OpenSource
Join the Alpha: jameskane.blog/genomics/202...
#RustLang #ATProto #OpenSource
Navigator Alpha: Run Your Own Genomics Lab on Your Own Machine
Navigator is the desktop app that turns your own computer into the analysis lab. Point it at a BAM, CRAM, or a raw data file from a consumer test, and it does the coverage, the Y and mitochondrial hap...
jameskane.blog
July 12, 2026 at 2:53 PM
Built in Rust with no complex dependencies, Navigator supports "progressive consensus" to cross-check multiple DNA kits & syncs anonymized results via AT Protocol for tree building.
Join the Alpha: jameskane.blog/genomics/202...
#RustLang #ATProto #OpenSource
Join the Alpha: jameskane.blog/genomics/202...
#RustLang #ATProto #OpenSource
Check it out at decoding-us.org/ytree?root=R....
Y-DNA Tree — Decoding Us
decoding-us.org
July 4, 2026 at 6:05 PM
Check it out at decoding-us.org/ytree?root=R....
The Formed and TMRCA ages are based on McDonald's (2021), Improved Models of Coalescence Ages of Y-DNA Haplogroups.
doi.org/10.3390/gene...
doi.org/10.3390/gene...
doi.org
July 4, 2026 at 6:05 PM
The Formed and TMRCA ages are based on McDonald's (2021), Improved Models of Coalescence Ages of Y-DNA Haplogroups.
doi.org/10.3390/gene...
doi.org/10.3390/gene...
Unlike prior examples, I did take pains to use FTDNA's labels where they are not obviously in need of improvement or don't exist.
The side panel shows the defining SNP(s) placements on b37, b38 and hs1 (chm13v2). Where available it also reconstructs the STR signature transitions from the parent.
The side panel shows the defining SNP(s) placements on b37, b38 and hs1 (chm13v2). Where available it also reconstructs the STR signature transitions from the parent.
July 4, 2026 at 6:05 PM
Unlike prior examples, I did take pains to use FTDNA's labels where they are not obviously in need of improvement or don't exist.
The side panel shows the defining SNP(s) placements on b37, b38 and hs1 (chm13v2). Where available it also reconstructs the STR signature transitions from the parent.
The side panel shows the defining SNP(s) placements on b37, b38 and hs1 (chm13v2). Where available it also reconstructs the STR signature transitions from the parent.
I have the 32GB model. When purchased in January, this was a no-brainer upgrade.
Like most SBCs the RAM is soldered on. It will be interesting to watch if this changes. Putting SODIMMs on the boards is the only way they will "beat" RAMogedden.
Like most SBCs the RAM is soldered on. It will be interesting to watch if this changes. Putting SODIMMs on the boards is the only way they will "beat" RAMogedden.
July 4, 2026 at 12:34 PM
I have the 32GB model. When purchased in January, this was a no-brainer upgrade.
Like most SBCs the RAM is soldered on. It will be interesting to watch if this changes. Putting SODIMMs on the boards is the only way they will "beat" RAMogedden.
Like most SBCs the RAM is soldered on. It will be interesting to watch if this changes. Putting SODIMMs on the boards is the only way they will "beat" RAMogedden.
With the used market having Ivy Bridge or newer systems like the Trashcan Mac going for $200 or less, it's hard to look at the SBCs here and their current pricing with RAM shortages as viable. Even if the Intels are using 10x the energy...
July 2, 2026 at 1:56 PM
With the used market having Ivy Bridge or newer systems like the Trashcan Mac going for $200 or less, it's hard to look at the SBCs here and their current pricing with RAM shortages as viable. Even if the Intels are using 10x the energy...
2. Strength: Structural variants. The graph recovers ~80% of HiFi SVs. Delly gets 26% on chr20 and collapses to 14% on chr16. The harder the region, the bigger the graph’s edge.
Full analysis: jameskane.blog/genomics/202... (3/3)
Full analysis: jameskane.blog/genomics/202... (3/3)
What a Pangenome Misses, and What It Nails
My last post argued that a genotype-only pangenome callset silently misses variation and quietly carries structural variation. This time I put numbers on both claims, across two whole chromosomes, wit...
jameskane.github.io
June 17, 2026 at 10:19 PM
2. Strength: Structural variants. The graph recovers ~80% of HiFi SVs. Delly gets 26% on chr20 and collapses to 14% on chr16. The harder the region, the bigger the graph’s edge.
Full analysis: jameskane.blog/genomics/202... (3/3)
Full analysis: jameskane.blog/genomics/202... (3/3)
1. Weakness: Small variants. The graph is blind to private SNPs because they aren't in the panel (99% representation gap). It also over-calls noise in repetitive regions (only 43% confirm). Standard linear callers win here. (2/3)
June 17, 2026 at 10:19 PM
1. Weakness: Small variants. The graph is blind to private SNPs because they aren't in the panel (99% representation gap). It also over-calls noise in repetitive regions (only 43% confirm). Standard linear callers win here. (2/3)