Hi all,
Following on our announcement of the first alpha release of the QIIME 2 Shotgun Metagenomics Distribution, we are starting to develop some alpha (early draft) tutorials. At the moment, we're going to keep these on GitHub and link to specific documents that you can view there. Before too long, we'll be starting to build and host Jupyter Books that cover tutorials for the different QIIME 2 distributions that are available.
We are very interested in feedback on our shotgun metagenomics workflows, so please don't hesitate to reach out - especially if we're doing something that seems wrong, or if you think you have a better approach.
Hi,
Still did not try metagenomic analyses in shotgun distribution, but I have a question regarding Nanopore sequences - is it possible to use qiime moshpit classify-kraken2 for Nanopore 16S reads?
Hi @Nicholas_Bokulich
Thank you for the reply.
On the resource page of Kraken2 indexes, I found Silva 132/138 and GG 13.5. I want to test it with the GG2 database to compare Nanopore classification with the GG2 plugin (similar to closed clustering), GG2 with blast and search classifiers, and now Kraken2 classification. For the last one, as I understood, I should build a database outside of qiime2. Can I import the database to qiime2, or do you mean to classify it outside as well and then import taxonomies ?
A shotgun (also known as a scattergun, peppergun,[1] or historically as a fowling piece) is a long-barreled firearm designed to shoot a straight-walled cartridge known as a shotshell, which discharges numerous small spherical projectiles called shot, or a single solid projectile called a slug. Shotguns are most commonly used as smoothbore firearms, meaning that their gun barrels have no rifling on the inner wall, but rifled barrels for shooting sabot slugs (slug barrels) are also available.
Shotguns come in a wide variety of calibers and gauges ranging from 5.5 mm (.22 inch) to up to 5 cm (2.0 in), though the 12-gauge (18.53 mm or 0.729 in) and 20-gauge (15.63 mm or 0.615 in) bores are by far the most common. Almost all are breechloading, and can be single barreled, double barreled, or in the form of a combination gun. Like rifles, shotguns also come in a range of different action types, both single-shot and repeating. For non-repeating designs, over-and-under and side-by-side break action shotguns are by far the most common variants. Although revolving shotguns do exist, most modern repeating shotguns are either pump action or semi automatic, and also fully automatic, lever-action, or bolt-action to a lesser extent.
Preceding smoothbore firearms (such as the musket) were widely used by European militaries from the 17th until the mid-19th century.[2] The muzzleloading blunderbuss, the direct ancestor of the shotgun, was also used in similar roles from self-defense to riot control. Shotguns were often favored by cavalry troops in the early to mid-19th century because of its ease of use and generally good effectiveness on the move, as well as by coachmen for its substantial power. But by the late 19th century, these weapons became largely replaced on the battlefield by breechloading rifled firearms shooting spin-stabilized cylindro-conoidal bullets, which were far more accurate with longer effective ranges. The military value of shotguns was rediscovered in the First World War, when American forces used the pump-action Winchester Model 1897 shotgun in trench fighting to great effect. Since then, shotguns have been used in a variety of close quarters combat roles in civilian, law enforcement, and military applications.
The smoothbore shotgun barrel generates less resistance and thus allows greater propellant loads for heavier projectiles without as much risk of overpressure or a squib load, and are also easier to clean. The shot pellets from a shotshell are propelled indirectly through a wadding inside the shell and scatter upon leaving the barrel, which is usually choked at the muzzle end to control the projectile scatter. This means each shotgun discharge will produce a cluster of impact points instead of a single point of impact like other firearms. Having multiple projectiles also means the muzzle energy is divided among the pellets, leaving each individual projectile with less penetrative kinetic energy. The lack of spin stabilization and the generally suboptimal aerodynamic shape of the shot pellets also make them less accurate and decelerate quite quickly in flight due to drag, giving shotguns short effective ranges. In a hunting context, this makes shotguns useful primarily for hunting fast-flying birds and other agile small/medium-sized game without risking overpenetration and stray shots to distant bystander and objects. However, in a military or law enforcement context, the high short-range blunt knockback force and large number of projectiles makes the shotgun useful as a door breaching tool, a crowd control or close-quarters defensive weapon. Militants or insurgents may use shotguns in asymmetric engagements, as shotguns are commonly owned civilian weapons in many countries. Shotguns are also used for target-shooting sports such as skeet, trap, and sporting clays, which involve flying clay disks, known as "clay pigeons", thrown in various ways by a dedicated launching device called a "trap".
For most of the history of the shotgun, the breechloading break-action shotgun was the most common type, and double-barreled variants are by far the most commonly seen in modern days. These are typically divided into two subtypes: the traditional "side-by-side" shotgun features two barrels mounted horizontally beside each other (as the name suggests), whereas the "over-and-under" shotgun has the two barrels mounted vertically one on top of the other. Side-by-side shotguns were traditionally used for hunting and other sporting pursuits (early long-barreled side-by-side shotguns were known as "fowling pieces" for their use hunting ducks and other waterbirds as well as some landfowls), whereas over-and-under shotguns are more commonly associated with recreational use (such as clay pigeon shooting). Both types of double-barrel shotgun are used for hunting and sporting use, with the individual configuration largely being a matter of personal preference.
Another, less commonly encountered type of break-action shotgun is the combination gun, which is an over-and-under design with one smoothbore barrel and one rifle barrel (more often with a rifle barrel on top, but a rifle barrel on bottom was not uncommon). There is also a class of break-action guns called drillings, which contain three barrels, usually two smoothbore barrels of the same gauge and a rifled barrel, though the only common theme is that at least one barrel be smoothbore. The most common arrangement was essentially a side-by-side shotgun with the rifled barrel below and centered. Usually a drilling containing more than one rifled barrel would have both rifled barrels in the same caliber, but examples do exist with different caliber barrels, usually a .22 long rifle and a centerfire cartridge. Although very rare, drillings with three and even four (a vierling) shotgun barrels were made.
In pump-action shotguns, a linearly sliding fore-end handguard (i.e. pump) is manually moved back-and-forth like a hand pump to work the action, extracting the spent shell and inserting a new round, while cocking the hammer or striker. A pump-action shotgun is typically fed from a tubular magazine underneath the barrel, which also serves as a guide rail for the pump. The rounds are fed in one by one through a port in the receiver, where they are lifted by a lever called the elevator and pushed forward into the chamber by the bolt. A pair of latches at the rear of the magazine hold the rounds in place and facilitate feeding of one shell at a time. If it is desired to load the gun fully, a round may be loaded through the ejection port directly into the chamber, or cycled from the magazine, which is then topped off with another round. Well-known examples include the Winchester Model 1897, Remington 870, and Mossberg 500/590.
Pump-action shotguns are common hunting, fowling and sporting shotguns. Hunting models generally have a barrel between 600 and 700 mm (24"-28"). Tube-fed models designed for hunting often come with a dowel rod or other stop that is inserted into the magazine and reduces the capacity of the gun to three shells (two in the magazine and one chambered) as is mandated by U.S. federal law when hunting migratory birds. They can also easily be used with an empty magazine as a single-shot weapon, by simply dropping the next round to be fired into the open ejection port after the spent round is ejected. For this reason, pump-actions are commonly used to teach novice shooters under supervision, as the trainer can load each round more quickly than with a break-action, while unlike a break-action the student can maintain his grip on the gun and concentrate on proper handling and firing of the weapon.
Early attempts at repeating shotguns invariably centred around either bolt-or lever-action designs, drawing inspiration from contemporary repeating rifles, with the earliest successful repeating shotgun being the lever-action Winchester M1887, designed by John Browning at the behest of the Winchester Repeating Arms Company.
Lever shotguns, while less common, were popular in the late 19th century with the Winchester Model 1887 and Model 1901 being prime examples. Initially very popular, demand waned after the introduction of pump-action shotguns around the start of the 20th century, and production was eventually discontinued in 1920.
One major issue with lever-actions (and to a lesser extent pump-actions) was that early shotgun shells were often made of paper or similar fragile materials (modern hulls are plastic or metal). As a result, the loading of shells, or working of the action of the shotgun, could often result in cartridges getting crushed and becoming unusable, or even damaging the gun.
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