Similar protocols

Pipeline publication

[…] illipore). DNA quantity and quality was checked photometrically using a NanoDrop ND-1000 UV/Vis spectral photometer (PeqLab, Germany) and by agarose gel electrophoresis. The products of the five MDA reactions were then pooled and used for whole genome sequencing., Amplified DNA was sequenced in two separate runs with 200 cycles on the Roche 454 FLX platform using Titanium chemistry. The average read length of the first run (310 Mbp) was 391 bp. The second run (235 Mbp) was a mate-pair library with 3 kbp inserts and had an average read length of 389 bp. All sequencing was performed at the SciLifeLab SNP/SEQ sequencing facility at Uppsala University. Contigs from both runs were assembled with Newbler using a minimal overlap of 40 bp and 90% identity., Phylogenetic binning of the contigs ≥1 kb was performed with PhylopythiaS () using the sample-specific model type. Additionally, contigs containing rRNA genes were identified by RNAmmer 1.2 (). The detected rRNA genes were phylogenetically assigned using the RDP Classifier (). All contigs assigned to the Epsilonproteobacteria were reordered with the Mauve Aligner () using the genome of Sulfurovum sp. NBC37-1 () as scaffold (acc. no. NC_009663)., Reordered contigs were uploaded to the Micro Scope platform (v. 2.5.4, May 2014; ) and automatically annotated. Automatic annotation was manually edited using the microbial annotation system Magnifying Genome (MaGe; ) that includes PsortB, SwissProt, TrEMBL, and COGnitor. Metabolic pathways were predicted using the integrated pathway tools of MaGe that are based on the KEGG and MicroCyc databases. Genome completeness was est […]

Pipeline specifications

Software tools Newbler, PPS, RNAmmer