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Pipeline publication

[…] b'n numbers CVNF01000001 to CVNF01000077 for P. ananatis S6, CVNG01000001 to CVNG01000071 for P. ananatis S7 and CVNH01000001 to CVNH01000061 for P. ananatis S8. The contigs were assembled using AMOScmp comparative assembler (Pop et al., ) and the Roche GS de novo assembler package (Newbler v2.6) in the 454 GS-FLXTM system (http://www.454.com/), indipendently. For AMOScmp assembly, four complete genomes of P. ananatis strains (P. ananatis AJ13355, P. ananatis LMG20103, P. ananatis LMG5342 and P. ananatis PA13) were used as potential reference genomes. As the assemblies based on P. ananatis AJ13355 resulted into highest coverage and mapping quality, this genome was used as reference genome for AMOScmp. The result of quality and coverage control of the assembly of each P. ananatis genome sequence was calculated using Qualimap v.1.0 (Garcia-Alcalde et al., ). In repetitive regions, such as rRNA operons, the assembly was further evaluated based on the read coverage distribution. Whole genome comparisons between P. ananatis S6, S7, and S8 strains were performed using Mauve v.2.3.1 (Darling et al., ). In Mauve, the Progressive Mauve algorithm was used to order the contigs against P. ananatis AJ13355 as reference genome. Genome assemblies are accessible via http://fileshare.csb.univie.ac.at/pantoea/., Five complete genomes of P. ananatis strains with different life styles and environmental origin were used in the comparative genomics and phylogenetic analysis. P. ananatis PA13 (accession numbers CP003085 and CP003086) is known as a pathogen of rice causing grain and sheath rot (Choi et al., ). P. ananatis AJ13355 (accession numbers AP012032 and AP012033) shows saprophytic life style and was isolated from soil (Hara et al., ). P. ananatis LMG20103 (accessio' […]

Pipeline specifications

Software tools AMOS, QualiMap, Mauve