Categories
BLOG

pipe vs

What is the difference between Pipe and Tube ?

People use the words pipe and tube interchangeably, and they think that both are the same. However, there are significant differences between pipe and tube.

The short answer is: A PIPE is a round tubular to distribute fluids and gases, designated by a nominal pipe size (NPS or DN) that represents a rough indication of the pipe conveyance capacity; a TUBE is a round, rectangular, squared or oval hollow section measured by outside diameter (OD) and wall thickness (WT), expressed in inches or millimeters.

What is Pipe ?

Pipe is a hollow section with round cross section for the conveyance of products. The products include fluids, gas, pellets, powders and more.

The most important dimensions for a pipe is the outer diameter (OD) together with the wall thickness (WT). OD minus 2 times WT (schedule) determine the inside diameter (ID) of a pipe, which determines the liquid capacity of the pipe.

Examples of actual O.D. and I.D.

Actual outside diameters

  • NPS 1 actual O.D. = 1.5/16″ (33.4 mm)
  • NPS 2 actual O.D. = 2.3/8″ (60.3 mm)
  • NPS 3 actual O.D. = 3½” (88.9 mm)
  • NPS 4 actual O.D. = 4½” (114.3 mm)
  • NPS 12 actual O.D. = 12¾” (323.9 mm)
  • NPS 14 actual O.D. = 14″ (355.6 mm)

Actual inside diameters of a 1 inch pipe.

  • NPS 1-SCH 40 = O.D.33,4 mm – WT. 3,38 mm – I.D. 26,64 mm
  • NPS 1-SCH 80 = O.D.33,4 mm – WT. 4,55 mm – I.D. 24,30 mm
  • NPS 1-SCH 160 = O.D.33,4 mm – WT. 6,35 mm – I.D. 20,70 mm

Such as above defined, the inside diameter is determined by the oudside diameter (OD) and wall thickness (WT).

The most important mechanical parameters for pipes are the pressure rating, the yield strength, and the ductility.

The standard combinations of pipe Nominal Pipe Size and Wall Thickness (schedule) are covered by the ASME B36.10 and ASME B36.19 specifications (respectively, carbon and alloy pipes, and stainless steel pipes).

What is Tube ?

The name TUBE refers to round, square, rectangular and oval hollow sections that are used for pressure equipment, for mechanical applications, and for instrumentation systems.

Tubes are indicated with outer diameter and wall thickness, in inches or in millimeters.

People use the words pipe and tube interchangeably, and they think that both are the same. However, there are significant differences between pipe and tube.

Pipe vs

GitHub is home to over 50 million developers working together to host and review code, manage projects, and build software together.

GitHub is where the world builds software

Millions of developers and companies build, ship, and maintain their software on GitHub — the largest and most advanced development platform in the world.

Use Git or checkout with SVN using the web URL.

Work fast with our official CLI. Learn more.

Launching GitHub Desktop

If nothing happens, download GitHub Desktop and try again.

Launching GitHub Desktop

If nothing happens, download GitHub Desktop and try again.

Launching Xcode

If nothing happens, download Xcode and try again.

Launching Visual Studio

Latest commit

Git stats

Files

Failed to load latest commit information.

README.md

V-pipe is a workflow designed for analysis of next generation sequencing (NGS) data from viral pathogens. It produces a number of results in a curated format.

Instructions to type in a shell

To obtain the installer for linux use the following:

Then, install miniconda,

To obtain the installer for MacOS, you can download it manually or use wget:

Then, install miniconda,

  1. Create conda virtual environment

Make sure to use source activate V-pipe everytime you want to run V-pipe

First, open a terminal and change into the working directory where input files are stored (i.e., the reference and the sequencing reads). We use a two-level directory hierarchy and we expect sequencing reads in a folder name raw_data . To initialize a project,

Before actually running the pipeline, we advise to check whether output files can be created from the inputs, using the –dryrun option.

Further details can be found in the wiki pages.

conda

Conda is a cross-platform package management system and an environment manager application.

Snakemake

Snakemake is the central workflow and dependency manager of V-pipe. It determines the order in which individual tools are invoked and checks that programs do not exit unexpectedly.

VICUNA

VICUNA is a de novo assembly software designed for populations with high mutation rates. It is used to build an initial reference for mapping reads with ngshmmalign aligner when a references/cohort_consensus.fasta file is not provided. Further details can be found in the wiki pages.

Other dependencies are managed by using isolated conda environments per rule, and below we list some of the computational tools integrated in V-pipe:

PRINSEQ

Trimming and clipping of reads is performed by PRINSEQ. It is currently the most versatile raw read processor with many customization options.

Vicuna

Vicuna is a de novo assembler designed for generating rough reference contigs of viral NGS data. It can deal with the inherent heterogeneity such as high single-base heterogeneity and structural variants.

ngshmmalign

We perform the alignment of the curated NGS data using our custom ngshmmalign that takes structural variants into account. It produces multiple consensus sequences that include either majority bases or ambiguous bases.

bwa

In order to detect specific cross-contaminations with other probes, the Burrows-Wheeler aligner is used. It quickly yields estimates for foreign genomic material in an experiment.

MAFFT

To standardise multiple samples to the same reference genome (say HXB2 for HIV-1), the multiple sequence aligner MAFFT is employed. The multiple sequence alignment helps in determining regions of low conservation and thus makes standardisation of alignments more robust.

Samtools

The Swiss Army knife of alignment postprocessing and diagnostics.

SmallGenomeUtilities

We perform genomic liftovers to standardised reference genomes using our in-house developed python library of utilities for rewriting alignments.

ShoRAH

ShoRAh performs SNV calling and local haplotype reconstruction by using bayesian clustering.

HaploClique and SAVAGE

We use HaploClique or SAVAGE to perform global haplotype reconstruction for heterogeneous viral populations by using an overlap graph.

Posada-Céspedes S., Seifert D., Topolsky I., Metzner K.J., and Beerenwinkel N. V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data. doi:10.1101/2020.06.09.142919

NOTE: During the Gibbs sampling performed by ShoRAH, several clusters may generate the same haplotype representative. Such collisions result in inflated posterior values. Also, the averaging of the haplotype abundances across iterations can be affected by floating-point precision problems. Fortunately, ShoRAH also reports the number of reads assigned to each haplotype per iteration which we use to correct the aforementioned quantities in post-processing. We are currently implementing the changes required to resolve these issues in future releases of ShoRAH.

  • Susana Posada Céspedes
  • David Seifert
  • Tobias Marschall
  • Niko Beerenwinkel

We encourage users to use the issue tracker. For further enquiries, you can also contact the V-pipe Dev Team [email protected]

About

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

V-pipe is a pipeline designed for analysing NGS data of short viral genomes – cbg-ethz/V-pipe ]]>