Computational protocol: Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces

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Protocol publication

[…] The de novo assembly was conducted using the CLC genomic workbench 6.0 (CLC Bio, Denmark) with sequences obtained from the Miseq system and the GS Assembler 2.6 (Roche Diagnostics, Branford, CT, USA) to sequences from the Roche 454 system. The hybrid assembly of generating contigs from both systems was performed using the CodonCode Aligner (CodonCode Co. Dedham, MA, USA). Gene prediction was performed using Glimmer 3 [], and the annotations were conducted by a homology search against Clusters of Orthologous Groups (COG) and the SEED database [,]. The comparative analyses of gene contents were performed using the RAST server []. The chromosomal region focusing fructooligosaccharide utilization in contig number 22 of strain DKU-01 was compared with synteny in similar organism using browse genome on the RAST server. The nucleotide similarities of msm operon were obtained by webcat (www.webact.org/WebACT/home) using BLASTN. […]

Pipeline specifications

Software tools CodonCode Aligner, Glimmer, RAST, WebACT, BLASTN
Application Genome data visualization
Organisms Clostridium butyricum, Homo sapiens, Clostridium butyricum 60E.3
Chemicals Carbohydrates, Butyric Acid