Arabidopsis P5C3

The dataset linked from this page contains the results of PacBio® SMRT® Sequencing for Arabidopsis thaliana Ler-0 as a resource for general community exploration. The genome was sequenced using P5-C3 chemistry and a 20 KB insert library with size selection performed using a 15kb-50 kb elution window protocol on a BluePippin™ DNA size-selection system from SAGE Science to generate 15.87 GB of unfiltered bases used for assembly.

Assembly of the genome was performed using HGAP2 and polished with Quiver. The results of the Celera assembly and the genome sequence after polishing with Quiver (see REFERENCE below) are also provided for those interested in the comparison. The preassembled reads were generated using a seed read cutoff of 17,254 bp. Only the polished assembly has been provided, while original data is available upon request.

Statistics:

Genome size: 124.6 Mb

GC content: 35.91%

Raw data: 15.87 Gb

Assembly Coverage: 18.74x

Polished Contigs: 545

Max Contig Length: 13.21 Mb

N50 Contig Length: 6.36 Mb

Sum of Contig Lengths: 130.86 Mb

The entire polished dataset can be downloaded here: http://datasets.pacb.com.s3.amazonaws.com/2014/Arabidopsis/reads/list.html

DESCRIPTION OF FILES

-polished-assembly.fasta

   Celera® Assembler genome assembly and QUIVER polished result.

-corrected.fasta

All Preassembled PacBio reads for direct input into Celera Assembler

-corrected.fastq

All preassembled PacBio reads for direct input into Celera Assembler with quality values

REFERENCE

Celera Assembler Resource: http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page

HGAP Bioinformatics Wiki: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP

HGAP Publication in Nature Methods: Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. Nat Methods. 2013 Jun;10(6):563-9. doi: 10.1038/nmeth.2474. Epub 2013 May 5.

Quiver Bioinformatics Wiki: https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/HowToQuiver.rst

Please also read supplemental section of the HGAP publication in Nature Methods for a better understanding of Quiver.