Genome in a Bottle Consortium
@genomeinabottle.bsky.social
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The Genome in a Bottle Consortium develops reference materials, reference data, and reference methods needed to benchmark human genome sequencing
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aphillippy.bsky.social
Adam Phillippy @aphillippy.bsky.social · 16d
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
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Genome in a Bottle Consortium @genomeinabottle.bsky.social · Jul 21
Our new draft V0.4 clonal/truncal somatic SV+CNV/CNA benchmark is at 42basepairs.com/browse/web/g.... Let us know if you have feedback to improve future versions!
data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.4-20250714 - Genome in a Bottle (FTP) - 42basepairs
42basepairs.com
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Genome in a Bottle Consortium @genomeinabottle.bsky.social · Jul 21
Our paper about extensive genomic data for a new broadly-consented pancreatic cancer cell line and matched normal tissue is now published at doi.org/10.1038/s415...! Stay tuned for draft GIAB benchmarks for somatic variants, and assemblies from these data coming soon! 1/2
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair - Scientific Data
Scientific Data - Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair
doi.org
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Reposted by Genome in a Bottle Consortium
resgen-io.bsky.social
resgen.io @resgen-io.bsky.social · Feb 4
Pssst 🤫... you can also try this live with @genomeinabottle.bsky.social data here:

resgen.io/paper-data/Z...
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Genome in a Bottle Consortium @genomeinabottle.bsky.social · Dec 20
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/ReferenceSam..., based on extensive short+long read sequencing data described in doi.org/10.1101/2024.... Feedback to improve future versions is very welcome!
Index of /ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar_DraftBenchmark_V0.1-20241219
ftp-trace.ncbi.nlm.nih.gov
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Reposted by Genome in a Bottle Consortium
aphillippy.bsky.social
Adam Phillippy @aphillippy.bsky.social · Apr 22
ModDotPlot preprint is now out! Winner of best poster at RECOMB 2023, it can generate either static or interactive dotplots in minutes using hierarchical modimizers. With @alexsweeten.bsky.social and @mikeschatz.bsky.social
Preprint: www.biorxiv.org/content/10.1...
Code: github.com/marbl/ModDot...
Animated GIF - Find & Share on GIPHY
Discover & share this Animated GIF with everyone you know. GIPHY is how you search, share, discover, and create GIFs.
media.giphy.com
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sedlazeck.bsky.social
Fritz Sedlazeck @sedlazeck.bsky.social · Nov 6
Tandem repeats are hard! Get your benchmark from
@genomeinabottle.bsky.social to compare caller

: biorxiv.org/content/10.1...

1.7 mil TR catalog; new tooling to overcome variant representation issues (SNV &SV); insight in complexity.

First time we can compare across different techs/caller!
Fig 3 from our preprint to highlight new benchmark approach capable of overcoming allele representation issues etc.
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Reposted by Genome in a Bottle Consortium
cdubsig.bsky.social
Corey Watson @cdubsig.bsky.social · Nov 1
New work from our group; curated long-read assemblies of the complex human IG kappa locus (with
@williamlees.bsky.social; vdjbase.org): www.biorxiv.org/content/10.1...
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Genome in a Bottle Consortium @genomeinabottle.bsky.social · Nov 1
Also a new Cancer GIAB page at www.nist.gov/programs-pro... with a data manifest that links to brand new ONT, Illumina, single cell, and Bionano data, with more coming soon
Genome in a Bottle Consortium @genomeinabottle.bsky.social · Nov 1
New preprints about GIAB tandem repeat benchmark www.biorxiv.org/content/10.1..., Chromosome X&Y benchmark www.biorxiv.org/content/10.1..., and stratifications www.biorxiv.org/content/10.1...
Genome in a Bottle Consortium @genomeinabottle.bsky.social · Nov 1
We are excited to release several new GIAB products in advance of #ASHG23, including v1.0 TR and X&Y benchmarks, corrected GRCh38 reference, stratifications for T2T-CHM13, RNA-seq, GIAB tumor/normal data, and a v1.0 T2T-HG002 assembly with #T2T. Details at www.nist.gov/programs-pro...
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