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The Python interpreter and the extensive standard library are freely availablein source or binary form for all major platforms from the Python web site, , and may be freely distributed. The same site alsocontains distributions of and pointers to many free third party Python modules,programs and tools, and additional documentation.
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The WOD is made up of ocean profiles, which contain measurements for a single variable (temperature, salinity, etc.) taken from one location at different depths, or a horizontal string of readings taken from the surface. WOD profiles must contain more than a single depth/variable pair. Multiple profiles taken at the same location with the same set of instruments form an oceanographic cast.
Temperature anomalies are calculated at 16 standard depths from 0-700m (or 26 standard depths 0-2000m) by subtracting observed (interpolated) temperatures from the long-term (1955-2018) climatological monthly mean. The mean of all temperature anomalies is calculated at each standard depth for every box on the grid. The temperature anomaly represents the volume of water that makes up the vertical distance from halfway between the next shallower depth and the given standard depth to halfway between the next deeper depth and the given standard depth.
Although our study necessarily addresses important technical details, its goal is to explore the full potential of the 16S gene for discriminating bacterial taxa rather than re-evaluate a particular sequencing technology. In addressing this goal, however, we highlighted the prevalence of sequencing errors in PacBio CCS reads as a factor that limits the ability to resolve highly similar sequences. A particular problem was deletion errors coincident with homopolymer runs in the target sequence. Although random sequencing errors may be overcome by increased sequencing depths, such systematic errors may occur at a given frequency and hence may not be improved by greater sequencing effort. Future work would benefit from explicitly determining how recent advances in sequencing platforms, chemistries, and computational approaches can improve these errors.
Reference 16S rRNA gene sequences matching strains in the mock community were initially downloaded from the RDP database40. Several reference gene sequences contained ambiguous base calls. Each sequence was therefore aligned to its respective WGS assembly and the aligned assembly region extracted to create an improved reference gene set containing a single representative 16S rRNA gene sequence for each member of the mock community.
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For grids that are the same from the smallest of devices to the largest, use the .col and .col-* classes. Specify a numbered class when you need a particularly sized column; otherwise, feel free to stick to .col. 041b061a72