Home of CB4856
(Courtesy Wil Shontell)

Welcome to the assembly hub for C. elegans Hawaiian strain CB4856!

You are viewing the contig-integrated genome.
This is the current reference assembly of CB4856, generated by iteratively integrating CB4856 variants into the N2 reference genome, then substituting de-novo contigs for recalcitrantly divergent regions wherever possible. Other assemblies on this hub include:

CB4856 Princeton Iterative Cycle 20, the iteratively edited CB4856 reference before integration of de novo contigs, with its associated annotation tracks
Reapr-processed JR-Assembler Contigs, the complete set of de novo contigs generated with the CB4856 Princeton dataset, including coverage depth in each of the 109 RIL/IL lines used to resolve contig mapping difficulties

UCSC Genome Browser assembly ID: CB4856Princeton_JR-contig
Assembly date: 2015
BioProject: PRJNA275000
BioSample: SAMN03334911
GenBank accession ID: JZEW00000000
Strain information: Strain CB4856

Track Hub Details:

Users accustomed to the C. elegans WS230 browser will be familiar with chromosome names beginning with "chr" (i.e. chrI, chrII, chrM, etc). In this browser we have elected to use chromosome names as they are more commonly seen in bioinformatic pipelines, without the "chr" prefix (i.e. I, II, MtDNA, etc). This has streamlined usage for the investigators, and we are hopeful it will not be problematic for general users.
Since this is a track hub (i.e. not a fully supported UCSC assembly) there is limited seach functionality. A blat server (nucleotide and translated) may facilitate navigation between WS230 and this assembly, but we are unfortunately unable to provide more search functions than these.

Download sequence and annotation data:

The CB4856 reference genome, along with supplementary data files, are available from the Waterston lab here. Supplementary files include (a) precise global alignments from CB4856 to WS230 using lastz, (b) all CB4856 SNVs with respect to WS230, (c) all CB4856 indels with respect to WS230, (d) a global summary of SNVs and indels, and (e) predicted effects of all variants vs. WS230.

The raw sequencing reads used to generate and annotate this reference are publically available here:

Andersen/Kruglyak Dataset, SRA experiment SRX1001806.
Waterston Dataset, SRA experiment SRX219150.
Yanai Dataset, SRA experiment SRX128707.
SOLiD sequencing of C. elegans recombinant lines (RILs), BioProject PRJEB7445.

News/Contact

Any questions, comments, and/or requests regarding this hub or its associated datasets should be directed to Owen Thompson or the Waterston Lab at the University of Washington.

July 1, 2015: Our paper is freely available via Open Access in the July 1, 2015 publication of Genetics.

May 19, 2015: Our paper is available Early Online here, doi: 10.1534/genetics.115.175950.

May 19, 2015: The CB4856 Hub is live!

A paper describing our full results and methods is available Early Online in the journal Genetics:

Remarkably divergent regions punctuate the genome assembly of the C. elegans Hawaiian strain CB4856

Owen A. Thompson*, L. Basten Snoek§, Harm Nijveen†, Mark G. Sterken§, Rita J.M. Volkers§, Rachel Brenchley‡, Arjen van ’t Hof‡, Roel P. J. Bevers**, Andrew R. Cossins‡, Itai Yanai§§, Alex Hajnal††, Tobias Schmid††, Jaryn D. Perkins‡‡, David Spencer*, Leonid Kruglyak***, Erik C. Andersen§§§, Donald G. Moerman‡‡, LaDeana W. Hillier*, Jan E. Kammenga§, Robert H. Waterston*

Afillilations:
*Department of Genome Sciences, University of Washington, Seattle WA 98195 USA
§Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
†Laboratory of Bioinformatics, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
‡Centre for Genome Research, Institute of Integrative Biology, Biosciences Building, University of Liverpool Crown Street, Liverpool L69 7ZB, United Kingdom
**Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
§§Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
††Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
‡‡ Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
*** Howard Hughes Medical Institute, Departments of Human Genetics and Biological Chemistry, David Geffen School of Medicine, U.C.L.A., Los Angeles, CA 90095
§§§ Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208