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Andrew Geoffrey Kaufman was an American entertainer, actor, writer, and performance artist. . Another well-known Kaufman character is Tony Clifton, an absurd, . programs hosted by or starring celebrities like Johnny Cash ( Christmas special), Dick She soon reunited with her mother, grandfather, uncle , and aunt. They're hardly ever offline and a mobile phone may as well have been placed in their hand at birth. “It's vital brands, ideas and messages. Florida's Spanish Flavor · Building Partnership for Improvement In Education · Building The · Chicago Latino Film Festival Movie · Chicago River: A River In Reverse .. Johnny Cash's Bitter Tears · Johnny Mathis - Wonderful Wonderful ( My Music Too: The Story of the Women's Airforce Service Pilots · We'll Meet Again.
Replicons not downloaded from NCBI may need their taxonomy information assigned explicitly. This can be done using the string kraken: For example, to put a known adapter sequence in taxon "synthetic construct"you could use the following: Once your library is finalized, you need to build the database.
Although D does increase as k increases, it is impossible to know exactly how many distinct k-mers will exist in a library for a given k without actually performing the count. The minimizers serve to keep k-mers that are adjacent in query sequences close to each other in the database, which allows Kraken to exploit the CPU cache.
Changing the value of M can significantly affect the speed of Kraken, and neither increasing or decreasing M will guarantee faster or slower speed. To build the database, you'll use the --build switch: The "--shrink" task allows you to take an existing Kraken database and create a smaller MiniKraken database from it.
The --shrink task is only meant to be run on a completed database. However, if you know before you create a database that you will only be able to use a certain amount of memory, you can use the --max-db-size switch for the --build task to provide a maximum size in GB for the database. This allows you to create a MiniKraken database without having to create a full Kraken database first.
A full list of options for kraken-build can be obtained using kraken-build --help. After building a database, if you want to reduce the disk usage of the database you can use kraken-build's --clean switch to remove all intermediate files from the database directory. To classify a set of sequences readsuse the kraken command: The files containing the sequences to be classified should be specified on the command line.
Note that to obtain optimum speeds, Kraken's database should be loaded into RAM first. This can be done through use of a ramdisk, if you have superuser permissions.
Failing that, you can use the --preload switch to kraken, e. See Memory Usage and Efficiency for more information.
The kraken program allows several different options: Use the --threads NUM switch to use multiple threads. Rather than searching all k-mers in a sequence, stop classification after the first database hit; use --quick to enable this mode.
Note that --min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome.
Classified or unclassified sequences can be sent to a file for later processing, using the --classified-out and --unclassified-out switches, respectively.
Kraken can handle gzip and bzip2 compressed files as input by specifying the proper switch of --gzip-compressed or --bzip2-compressed. If regular files are specified on the command line as input, Kraken will attempt to determine the format of your input prior to classification.
Kraken does not query k-mers containing ambiguous nucleotides non-ACGT. If you have paired reads, you can use this fact to your advantage and increase Kraken's accuracy by concatenating the pairs together with a single N between the sequences.
Using the --paired option when running kraken will automatically do this for you; simply specify the two mate pair files on the command line.
We have found this to raise sensitivity by about 3 percentage points over classifying the sequences as single-end reads. Each sequence classified by Kraken results in a single line of output. Output lines contain five tab-delimited fields; from left to right, they are: The taxonomy ID Kraken used to label the sequence; this is 0 if the sequence is unclassified.
The length of the sequence in bp. A space-delimited list indicating the LCA mapping of each k-mer in the sequence. The script operates on the output of kraken, like so: The first column of kraken-translate's output are the sequence IDs of the classified sequences, and the second column contains the taxonomy of the sequence.
For example, an output line from kraken of: C SEQ1 36 SEQ1 root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli Alternatively, kraken-translate accepts the option --mpa-format which will report only levels of the taxonomy with standard rank assignments superkingdom, kingdom, phylum, class, order, family, genus, speciesand uses pipes to delimit the various levels of the taxonomy.
Paired Reads Kraken will classify paired reads when the user specifies the --paired option by first concatenating the reads using before classifying the combined reads against the Kraken database. A number of other options are included in Kraken v1. The following describes these options and lists the possible combinations of these options and their behavior when applied. Memory Usage and Efficiency Kraken's execution requires many random accesses to a very large file.
To obtain maximal speed, these accesses need to be made as quickly as possible. This means that the database must be in physical memory during execution. Although we provide the --preload option to Kraken for users who cannot use a ramdisk, the ramdisk is likely the simplest option, and is well-suited for installations on computers where Kraken is to be run a majority of the time.
In addition, using a ramdisk allows the initial start-up of Kraken to be accomplished much more quickly. If a ramdisk is used, the --preload switch should not be used. We also note that in some cases, --preload may not be needed or even advisable. If you know that your database is already in memory for example, if it has been recently read or unzipped, then it should be in your operating system cache, which resides in physical memorythen there is no need to perform this step.
The selection of the best way to get the database into memory is dependent on several factors, including your total amount of RAM, operating system, and current free memory. For this reason, you may need to experiment with your own setup to find a good solution for you.
To create a ramdisk, you will need to have superuser root permission. As root, you can use the following commands to create a ramdisk: In that case, you'll need to make that user the owner of the directory via chown.
To put the database on the ramdisk, simply copy the database directory to the ramdisk directory: Note that when using the --paired option, Kraken will not by default make any attempt to ensure that the two files you specify are indeed matching sets of paired-end reads. To verify that the names of each read do indeed match, you can use the --check-names option in combination with the --paired option.
To get an idea as to Kraken's results across an entire sample, we provide the kraken-report script.
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It is used like this: Output is sent to standard output. The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows: Percentage of reads covered by the clade rooted at this taxon Number of reads covered by the clade rooted at this taxon Number of reads assigned directly to this taxon A rank code, indicating U nclassified, D omain, K ingdom, P hylum, C lass, O rder, F amily, G enus, or S pecies.
All other ranks are simply '-'.
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NCBI taxonomy ID indented scientific name The scientific names are indented using spaces, according to the tree structure specified by the taxonomy. By default, taxa with no reads assigned to or under them will not have any output produced. However, if you wish to have all taxa displayed, you can use the --show-zeros switch to do so. This can be useful if you are looking to do further downstream analysis of the reports, and want to compare samples.
Sorting by the taxonomy ID using sort -nf5 can provide a consistent line ordering between reports.
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In addition, we also provide the program kraken-mpa-report; this program provides output in a format similar to MetaPhlAn's tab-delimited output. For kraken-mpa-report, multiple Kraken output files can be specified on the command line and each will be treated as a separate sample.
For each taxon at the standard ranks from domain to speciesthe count of reads in each sample assigned to any node in the clade rooted at that taxon is displayed. Confidence Scoring At present, we have not yet developed a confidence score with a solid probabilistic interpretation for Kraken. January Main article: Tony Clifton Another well-known Kaufman character is Tony Clifton, an absurd, audience-abusing lounge singer who began opening for Kaufman at comedy clubs and eventually even performed concerts on his own around the country.
Sometimes it was Kaufman performing as Clifton, sometimes it was his brother Michael or Zmuda.
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For a brief time, it was unclear to some that Clifton was not a real person. News programs interviewed Clifton as Kaufman's opening act, with the mood turning ugly whenever Kaufman's name came up. Kaufman, Clifton insisted, was attempting to ruin Clifton's "good name" in order to make money and become famous. As a requirement for Kaufman's accepting the offer to star on Taxi, he insisted that Clifton be hired for a guest role on the show as if he were a real person, not a character.
Much to Kaufman's delight, this incident was reported in the local newspapers. At the end of the show, she stood up, took her mask off and revealed to the audience that she was actually comedian Robin Williams in disguise. He invited anyone interested to meet him on the Staten Island Ferry the next morning, where the show continued.
He came up with Andy's Funhouse, based on an old routine he had developed while in junior college. The special was taped in but did not air until August The segment was just over six minutes long and was called Uncle Andy's Funhouse. It featured Kaufman as the host of a children's show for adults, complete with a peanut gallery and Tony Clifton puppet. It too featured a peanut gallery, and opened in the middle of an interview Kaufman is doing in which he is laughing hysterically.
He then proceeds to thank the audience for watching and the credits roll. In his first appearance, during a sketch about four people out on a dinner date who excuse themselves to the restroom to smoke marijuanaKaufman broke character and refused to say his lines. Co-producer Jack Burns stormed onto the stage, leading to a brawl on camera before the show abruptly cut away to a commercial. Later that year, Kaufman returned to host Fridays.
At one point in the show, he invited a Lawrence Welk Show gospel and standards singer, Kathie Sullivanon stage to sing a few gospel songs with him and announced that the two were engaged to be married, then talked to the audience about his newfound faith in Jesus Kaufman was Jewish.
That was also a hoax. Instead of introducing the band, he delivered a nervous speech about the harmfulness of drugs while the band stood behind him ready to play. After his speech, he informed the audience that he had talked for too long and had to go to a commercial.
Jim Carreywho revealed the secret, later went on to play Kaufman in the film Man on the Moon. In a interview with the Memphis Flyer, Lawler said he had improvised during their first match and the Letterman incident.
Although officials at St. Sometimes, Lawler detailed how they came up with the angle and kept it quiet.
Even though Kaufman's injury was legitimate, the pair exaggerated it. He also said that Kaufman's furious tirade and performance on Letterman was Kaufman's own idea, including when Lawler slapped Kaufman out of his chair.
Promoter Jerry Jarrett later recalled that for two years, he would mail Kaufman payments comparable to what other main-event wrestlers were getting at the time, but Kaufman never deposited the checks.
The film was a parody of the art film My Dinner with Andre. Lynne Margulies, sister of the film's director, Johnny Legendappears in it, and became romantically involved with Kaufman. InKaufman became a playable character in the video game Legends of Wrestling II and a standard character in 's Showdown: InJakks Pacific produced for their WWE Classic Superstars toy line an action figure two-pack of Kaufman and Lawler, as well as a separate figures release for each of them.
After he angered the audience with his female-wrestling routine, Kaufman in January made a pretaped appearance his 16th asking the audience if he should ever appear on the show again, saying he would honor their decision.