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If you are assembling PacBio or Oxford Nanopore data, please use Canu instead. Celera Assembler is no longer being maintained.

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). The pipeline revised for PacBio/Oxford was named 'PBcR' (Berlin 2015).

Celera Assembler can use any combination of reads from:

Resources

Downloads

User guides

Examples

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.
  • PBcR - A correction and assembly pipeline for high-noise single-molecule sequencing data. 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.

Events

CA 8.3 Release

Celera Assembler 8.3rc2 was released on 24 May, 2015. Download. Release notes. Errata.

CA 8.2 Release

Celera Assembler 8.2 was released on 12 November, 2014. Download. Release notes. Change log. Errata.

CA 8.2 Beta Release

Celera Assembler 8.2 beta was released on 19 July, 2014. Download. Release notes. Change log. Errata.

CA 8.1 Release

Celera Assembler 8.1 was released on 16 December, 2013. Download. Release notes. Change log. Errata.

CA 8.0 Release

Celera Assembler 8.0 was released on 5 November, 2013. Download. Release notes. Change log. Errata.

CA 7.0 Release

Celera Assembler 7.0 was released on January 12, 2012. Download. Release notes. Change log. Errata. See also Best Practices.

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, errata, 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