Sequencing the Bonobo Genome
نویسندگان
چکیده
The Bonobo Genome Consortium generated DNA sequencing reads representing the genome of a single bonobo individual. The data consisted of almost 270 million fragment sequences generated on FLX machines from 454 Life Sciences. The fragments derived from FLX standard and Titanium chemistries, and from paired and unpaired protocols. The data was assembled at the J. Craig Venter Institute with the open-source Celera Assembler software including the CABOG variant designed for pyrosequencing data. The assembly process combined reads and paired end constraints into contigs and scaffolds. Considering all reads that survived minimum length and quality filters, the assembly incorporated 88% of reads and satisfied 86% of the usable mate pair constraints while violating only 0.12%. The assembled scaffolds had a combined length that approaches the expected 3 Gbp genome size. General Assembly Parameters Two assemblies were generated with the Celera Assembler software, also known as CABOG [59]. The specific software version, 5.4.3, is available from the Source Forge web site (http://wgsassembler.sourceforge.net) as a packaged release. It is also tagged VERSION-5_43-RELEASE in the cvs source code repository on Source Forge. Celera Assembler was run with the algorithmic parameter settings given in Table S2.1. The expected sequencing error rate (utgErrorRate, default=0.015) was adjusted upwards based on preliminary analysis of other Titanium reads, not shown. The limit on iterations of scaffold operations (doExtendClearRange, default=2) was chosen to reduce run time. The assembly process ran on a compute grid running Linux and SGE at the J. Craig Venter Institute. The total assembly pipeline used about 2.5 TB of disk. The parallel computes ran on grid nodes with 2 to 4 core and 8 to 16 GB RAM. The non-parallel computes ran on a single 16core node with 96GB shared RAM. The performance-related parameter settings are given in Table S2.2. WWW.NATURE.COM/NATURE | 8 SUPPLEMENTARY INFORMATION RESEARCH doi:10.1038/nature11128
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