Similar protocols

Pipeline publication

[…] medium) [] at 20 °C. Genomic DNA was isolated using a Power Soil DNA Isolation kit (MoBio) following the standard protocol provided by the manufacturer but modified by the addition of 100 μl Tris for cell lysis. DNA is available from DSMZ through DNA Bank Network []., The draft genome sequence was generated using Illumina sequencing technology. For this genome, we constructed and sequenced an Illumina paired-end library with the Illumina Nextera XT library preparation kit and sequencing of the library using Genome Analyzer IIx were performed as described by the manufacturer (Illumina, San Diego, CA, USA). A total of 4.6 million paired-end reads were derived from sequencing and trimmed using Trimmomatic version 0.32 []. De novo assembly of all trimmed reads with SPAdes version 3.5.0 [] resulted in 227 contigs and 150-fold coverage., Genes were identified as part of the genome annotation pipeline of the Integrated Microbial Genomes (IMG-ER) platform using Prodigal v2.50 []. The predicted CDS were translated used to search the CDD, KEGG, UniProt, TIGRFam, Pfam and InterPro databases. These data sources were combined to assert a product description for each predicted protein. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [], RNAmmer [], Rfam [], TMHMM [] and SignalP []. Additional gene prediction analyses and functional annotation were performed within the IMG-ER platform []., The genome consists of 227 contigs with a total length of 4,106,736 bp and a G + C content of 53.77% (Table ). Of the 4166 genes predicted, 4128 were protein-coding genes, and 38 RNA genes. No pseudogenes or CRISPR elements were found. For t […]

Pipeline specifications

Software tools Trimmomatic, SPAdes, Prodigal