Computational protocol: Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi

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Protocol publication

[…] Purified DNA was sequenced in a 454 pyrosequencer (GS FLX+, Roche) at the Genomics Core Facility of the Huck Institutes of the Life Sciences at The Pennsylvania State University. A total of 554,976 paired-end reads were generated and assembled by Newbler assembler (Roche) into one large scaffold comprising 88 contigs and 34 stand-alone contigs of 500 bp or larger with an average read depth of ∼40×. Further assembly and gap closing was managed using the phred/phrap/consed package (Ewing et al., ; Gordon et al., ). PCR products covering gaps between contigs were obtained by following suggestions from paired-end reads or by combinatorial PCR and were sequenced. Potential frame shifts were predicted using GeneTack (Antonov and Borodovsky, ) and either confirmed or corrected after resequencing or were modified after re-examining and editing the original assembly. The genome was annotated using a pipeline based on FGENESB software (Softberry, Inc., USA), Artemis (Sanger Institution, UK), and custom-made Perl scripts (ActivePerl; ActiveState Inc., Vancouver, BC, USA). The rRNA genes were annotated using RNAmmer 1.2 software (Lagesen et al., ). Naming of proteins was based primarily on the KEGG database and on recommendations by GenBank. The genome sequence has been deposited in GenBank and has been assigned the accession number CP003418. […]

Pipeline specifications

Software tools Newbler, Consed, FGENESB, RNAmmer
Databases GeneTack KEGG
Application Genome annotation
Organisms Ignavibacterium album
Chemicals Sulfur