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GainsboroOrangeVISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP

Tallymer-mkindex

Community rating: ?????

Tallymer-mkindex is used for counting and indexing k-mers for a specified value of k (e.g. all 20-mers) in a set of sequences. Requires an enhanced suffix array (ESA) generated using Suffixerator. Output is a Tallymer index that can be used for searching fasta sequences using the app Tallymer-Search.

Quick Start

To use Tallymer-mkindex, you must specify an ESA that was generated with Suffixerator. Specify a particular length of k-mer that you want indexed, such as '20' for 20-mers. Also specify the minimum occurrence count of k-mer required for reporting. For example if you want all k-mers reported, including single copy, you would enter '1'. If you only want to include k-mers that occur five or more times in the ESA then enter '5'.

Resources:

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Tallymer.

Input File(s)

Specify the directory containing the ESA files. For example if you use the above example_data directory then the entry will end up being "/iplant/home/shared/iplantcollaborative/example_data/Tallymer/".

Then specify the root name of the ESA. Using example_data you would enter "maize_BAC100".

Parameters Used in App

Use these parameters within the DE app interface:
- Desired k-mer length: specify a number indicating k-mer length to be indexed
- Minimum occurance of k-mer to report: specify a number indicating the minimum number of times a k-mer must be found in the original set of sequences used to generate the Suffixerator ESA, in order to be indexed. For example if you specify '5' then only k-mers found 5 or more times in the original set of sequences used to generate the Suffixerator ESA will be indexed.
- Give a name to the index you are creating (optional). Provide a root name for the index to be generated or the app will generate a name automatically. In the example we provided the root name "maize_BACS100_20mer_minocc5" to indicate the original source of sequence, the desired k-mer length, and the minimum occurrence count.

Output File(s)

Output will be four files:

maize_BACS100_20mer_minocc5.mbd
maize_BACS100_20mer_minocc5.mct
maize_BACS100_20mer_minocc5.mer
mer20distribution

The first 3 files listed above together constitute the tallymer index. These files have a common root name and unique 3-letter suffix.

The mer20distribution file is a text file that gives summary information about about distribution of k-mers.

Tool Source for App

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Requires an enhanced suffix array (ESA) generated using Suffixerator. Output is a Tallymer index that can be used for searching fasta sequences using the app Tallymer-Search.","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Quick Start","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"To use ","type":"text"},{"text":"Tallymer-mkindex","type":"text","marks":[{"type":"strong"}]},{"text":", you must specify an ESA that was generated with Suffixerator. Specify a particular length of k-mer that you want indexed, such as '20' for 20-mers. Also specify the minimum occurrence count of k-mer required for reporting. For example if you want all k-mers reported, including single copy, you would enter '1'. If you only want to include k-mers that occur five or more times in the ESA then enter '5'.","type":"text"}]}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Resources:","type":"text","marks":[{"type":"strong"}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/tallymer.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/tallymer.html"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://www.zbh.uni-hamburg.de/fileadmin/gi/tallymer/tallymer.pdf","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.zbh.uni-hamburg.de/fileadmin/gi/tallymer/tallymer.pdf"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://genometools.org/","type":"text","marks":[{"type":"link","attrs":{"href":"http://genometools.org/"}}]}]}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Test Data","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Test data for this app appears directly in the Discovery Environment in the Data window under ","type":"text"},{"text":"Community Data -> iplantcollaborative -> example_data ->","type":"text","marks":[{"type":"em"}]},{"text":" ","type":"text"},{"text":"Tallymer","type":"text","marks":[{"type":"em"},{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":".","type":"text"}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Input File(s)","type":"text"}]},{"type":"paragraph","content":[{"text":"Specify the directory containing the ESA files. For example if you use the above example_data directory then the entry will end up being \"/iplant/home/shared/iplantcollaborative/example_data/Tallymer/\".","type":"text"}]},{"type":"paragraph","content":[{"text":"Then specify the root name of the ESA. Using example_data you would enter \"maize_BAC100\".","type":"text"}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Parameters Used in App","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Use these parameters within the DE app interface:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Desired k-mer length: specify a number indicating k-mer length to be indexed","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Minimum occurance of k-mer to report: specify a number indicating the minimum number of times a k-mer must be found in the original set of sequences used to generate the Suffixerator ESA, in order to be indexed. For example if you specify '5' then only k-mers found 5 or more times in the original set of sequences used to generate the Suffixerator ESA will be indexed.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Give a name to the index you are creating (optional). Provide a root name for the index to be generated or the app will generate a name automatically. In the example we provided the root name \"maize_BACS100_20mer_minocc5\" to indicate the original source of sequence, the desired k-mer length, and the minimum occurrence count.","type":"text"}]}]}]}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Output File(s)","type":"text"}]},{"type":"paragraph","content":[{"text":"Output will be four files:","type":"text"}]},{"type":"paragraph","content":[{"text":"maize_BACS100_20mer_minocc5.mbd","type":"text"},{"type":"hardBreak"},{"text":" maize_BACS100_20mer_minocc5.mct","type":"text"},{"type":"hardBreak"},{"text":" maize_BACS100_20mer_minocc5.mer","type":"text"},{"type":"hardBreak"},{"text":" mer20distribution","type":"text"}]},{"type":"paragraph","content":[{"text":"The first 3 files listed above together constitute the tallymer index. These files have a common root name and unique 3-letter suffix.","type":"text"}]},{"type":"paragraph","content":[{"text":"The mer20distribution file is a text file that gives summary information about about distribution of k-mers.","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Tool Source for App","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/tallymer.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/tallymer.html"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://www.zbh.uni-hamburg.de/fileadmin/gi/tallymer/tallymer.pdf","type":"text","marks":[{"type":"link","attrs":{"href":"http://www.zbh.uni-hamburg.de/fileadmin/gi/tallymer/tallymer.pdf"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"http://genometools.org/","type":"text","marks":[{"type":"link","attrs":{"href":"http://genometools.org/"}}]}]}]}]}]}]}]}]}],"version":1}}}},{"text":" ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]},{"type":"paragraph"}],"version":1}

Tallymer-mkindex (archived)

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