PMC:3111987 / 9435-11416 JSONTXT

{"project":"2_test","denotations":[{"id":"21677857-18349386-140427634","span":{"begin":620,"end":622},"obj":"18349386"},{"id":"21677857-21304632-140427635","span":{"begin":1331,"end":1333},"obj":"21304632"}],"text":"Genome sequencing and assembly\nThe genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [37]. Pyrosequencing reads were assembled using the Newbler assembler version 2.3-PreRelease-10-21-2009 (Roche). The initial Newbler assembly consisting of 57 contigs in eight scaffolds was converted into a phrap [38] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (2,241.8 Mb) was assembled with Velvet, version 0.7.63 [39] and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 138 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package [38] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution [37], Dupfinisher, or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI) [40]. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F.Chang, unpublished). A total of 65 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI [41]. The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 552.5 × coverage of the genome. The final assembly contained 389,415 pyrosequence and 33,128,505 Illumina reads."}