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*Denisov et al. (2008) [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/8/1035 Consensus Generation and Variant Detection by Celera Assembler.] Bioinformatics 24(8):1035-40
*Denisov et al. (2008) [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/8/1035 Consensus Generation and Variant Detection by Celera Assembler.] Bioinformatics 24(8):1035-40
*Miller et al. (2008) [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn548 Aggressive Assembly of Pyrosequencing Reads with Mates.] Bioinformatics 24(24):2818-2824
*Miller et al. (2008) [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn548 Aggressive Assembly of Pyrosequencing Reads with Mates.] Bioinformatics 24(24):2818-2824
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*Salzberg et al. (2004) [http://www.biomedcentral.com/1471-2164/9/204 Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae] BMC Genomics.
*Zimin et al. (2009) [http://genomebiology.com/2009/10/4/R42 A whole-genome assembly of the domestic cow, Bos taurus.] Genome Biology 10:R42
*Zimin et al. (2009) [http://genomebiology.com/2009/10/4/R42 A whole-genome assembly of the domestic cow, Bos taurus.] Genome Biology 10:R42
*Miller et al. (2009) Shotgun Assembly of a Repetitive Plant Genome. [[Cucumber Poster]]
*Miller et al. (2009) Shotgun Assembly of a Repetitive Plant Genome. [[Cucumber Poster]]

Revision as of 13:46, 1 May 2013

Celera Assembler : scientific software for biological research. Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing. Celera Assembler has enabled many advances in genomics, including the first whole genome shotgun sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celera Genomics starting in 1999. It was released to SourceForge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was named CABOG (Miller 2008).

Celera Assembler can use any combination of reads from:

Resources

User guides

Input formats

The Celera Assembler expects input fragment data to be in the FRG format. We provide several utilities for converting a variety of data types into this format:

  • fastaToCA - converts sequence and quality values in fasta format.
  • tracearchiveToCA - converts xml, qual and fasta from the NCBI TraceDB into FRG format.
  • sffToCA - converts 454 SFF files into FRG format, optionally searching each read for 'linker' sequence indicating the read is a pair of mated reads.
  • fastqToCA - generates a FRG file that allows direct loading of Illumina FastQ files.
  • pacBioToCA - A correction pipeline for PacBio RS sequencing data. Uses short-read technologies to generate high-accuracy consensus for PacBio RS sequences. The output is a FRG file (along with fasta and qual).

Output formats

  • ASM Files = The Celera Assembler native output format.
  • QC Metrics = The statistical summary.
  • POSMAP = Positional maps in perl-friendly text files.
  • FASTA Files = With consensus sequence and quality values.

Downloads

Start by downloading a tested release package. Releases include pre-compiled binaries for Linux. Adventurous users are welcome to check out any version of the source code (including what is currently in development), compile it, and hope for the best.

Events

CA 7.0 Release

Celera Assembler 7.0 was released on January 12, 2012. Download. Read the release notes. See the change log. Find any known problems.

Mailing List

Users of Celera Assembler are encouraged to sign up to the wgs-assembler-users mailing list. The list is intended for discussion on using Celera Assembler. We'll announce new releases, new features and bug fixes too. Bug reports should still be reported to the bug tracker.

User Group Meeting: Jan 2012

The J. Craig Venter Institute will host the CAUG 2012 Celera Assembler User Group Meeting Thursday & Friday, 12-13 January 2012. Contact us about registration (ATGatJCVIdotORG). The format will be similar to the CAUG 2010 of 26-27 August 2010. Thanks to all 30 participants from around the world, and to the U.S. National Institute of General Medical Sciences (NIGMS) for funding.

CA 6.1 Release

Celera Assembler 6.1 was released on April 30th, 2010. This is the first version with support for Illumina sequence data. See Releases, fastq support, release notes, the change log, known problems, and test results.

Internship Opportunity

The J. Craig Venter Institute will hire summer interns to work on a variety of scientific endeavors including the Celera Assembler software. Students at the graduate, undergraduate, and high school levels should apply through the JCVI Internship Program. Funding for Celera Assembler internships is provided by a grant from the National Institute of General Medical Sciences (NIGMS). It is too late to apply for a summer 2011 position so please apply in regard to future semesters.

Publications

Sponsors

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