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Anonymous Sergey Koren Jason Miller Brian Walenz Michal Kotelba

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:



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 only PacBio RS sequences or short-read technologies to generate high-accuracy consensus. The output is a FRG file (along with fasta and qual).

Output formats


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.




Wiki: ASM_Files
Wiki: Best_Practices
Wiki: Bonobo_Poster
Wiki: CAUG_2010
Wiki: CAUG_2012
Wiki: Cucumber_Poster
Wiki: Developers
Wiki: Escherichia_coli_K12_MG1655,_using_uncorrected_PacBio_reads,_with_CA8.1
Wiki: FASTA_Files
Wiki: FastaToCA
Wiki: FastqToCA
Wiki: Help
Wiki: PBcR
Wiki: PacBioToCA
Wiki: Pair_classification_within_Illumina_mate_pair_data
Wiki: Porphyromonas_gingivalis_W83,_using_454_3_Kbp_mated_reads,_with_CA8.1
Wiki: QC_Metrics
Wiki: Requirements
Wiki: RunCA
Wiki: RunCA_Dissection
Wiki: SffToCA
Wiki: TracearchiveToCA
Wiki: Utilities
Wiki: Yersinia_pestis_KIM_D27,_using_454_8_Kbp_mated_reads,_with_CA8.1
Wiki: Yersinia_pestis_KIM_D27,_using_Illumina_paired-end_reads,_with_CA8.1