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From  Tue Apr 17 22:02:19 2018
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From: "Rosen, Ben - ARS" <Ben.RosenARS.USDA.GOV> 
Postmaster: submission approved by list moderator
To: Members of AnGenMap <>
Subject: Bovine reference assembly ARS-UCD1.2
Date: Tue, 17 Apr 2018 22:02:20 -0500

Dear cattle community,

We are pleased to announce the release of the new bovine reference assembly
ARS-UCD1.2. It is available for download at NCBI through the following

Approximately 80x genome coverage of PacBio sequence was de novo assembled
with Falcon, this was followed by scaffolding with Dovetail Genomics
Chicago data, the BtOM1.0 Optical Map and a recombination map of 59K
autosomal SNPs yielding chromosome length scaffolds. The scaffolded
assembly was then refined with independent de-novo assemblies from CANU and
MaSuRCA, error corrected with an independent genetic map, and polished with
50x Illumina reads. Assembly statistics include an N50 contig size of 26 Mb
with 387 gaps representing many fold improvements over UMD3.1 (contig
N50=0.097 Mb, 72,051 gaps). Additionally, full-length transcripts from 28
Dominette tissues have been sequenced with PacBio using the Iso-Seq method
to support improved annotation to be released shortly.

To facilitate the transition from UMD3.1 we will be providing annotation
liftOver coordinates and a liftOver chain file. Additionally, we have
updated SNP marker mappings using probe information and flanking sequence
information for most of the available assays from Geneseek, Zoetis,
Weatherbys and Affymetrix. We intend on providing these as plink map files
as well as raw csv files.

This assembly was supported by funding from NRSP8 Coordinator Funds,
USDA/MARC and donations from Neogene and Zoetis. We would additionally like
to acknowledge the contributions of Richard Hall and Elizabeth Tsang
(PacBio), Christian Dreischer (Computomics), Aleksey Zimin (UMD), and
Christine Elsik (MU). Please address inquiries about the assembly to

 Ben Rosen
 Derek Bickhart
 Bob Schnabel
 Sergey Koren
 Tim Smith
 Juan Medrano

Benjamin D Rosen
Research Biologist (Computational), ARS, USDA
Animal Genomics and Improvement Laboratory
Building 306, Room 112, BARC-East
10300 Baltimore Ave
Beltsville, MD 20705-2350
TEL: 301.504.8416
CELL: 530.574.4761
SKYPE: bdrosen22
FAX: 301.504.8414

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