Similar protocols

Pipeline publication

[…] its member contigs. We herein incorporated contig length as a scaling factor in the calculation and thereby obtained the weighted arithmetic mean of the cluster’s depth of coverage and weighted standard deviation of the same as defined below., Depth of coverage of contig i, (2)xi= N×Lwi weighted mean depth of coverage of cluster j (3)x¯j= ∑i=1nwi×xi∑i=1nwi and weighted standard deviation of the depth of coverage of cluster j (4)σ¯j= ∑i=1nwi×(xi−x¯j)2∑i=1nwi as used in this study, where N = number of reads mapped to contig i, L = average read length, xi = depth of coverage of contig i, weight wi = length of contig i and n = the number of contigs in cluster j., Mapping was performed using the Burrows-Wheeler Alignment tool (BWA) []. Prior to mapping, reads were quality trimmed (specifics may be found in ), however, duplicates were not removed as had been done for the assembly., Putative genes were predicted in both grouped and un-grouped contigs. Nineteen near complete draft genomes were submitted to the annotation server RAST [] for functional annotation. Additionally, gene calling was performed on all contigs using the GeneMarkS algorithm [], followed by a BLAST search against NCBI’s non-redundant protein database to infer annotation from existing homologs and achieve an overview of the functions present in the phage cocktail. Annotation was hereby extracted from the top BLAST hit with the additional requirement that the match to this top hit had an E-value smaller than or equal to 1 × 10−10. The results of the two approaches were then compared. Two genes were considered to be the same if their start and end coordinates were less than 10% of the gene length apart and in frame of each other; that is, if the difference between the coordinates for the two genes was a multiple of three. The obtained annotation […]

Pipeline specifications

Software tools BWA, RAST, GeneMarkS