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Tallymer-search

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Identify k-mers in a file of input fasta sequences that are represented in a tallymer-index. Requires a tallymer index generated using Tallymer-mkindex. Output shows k-mer, its position in the searched fasta file, and its occurance count in the index.

Quick Start

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Test Data

Info

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 fasta file that you want to search.  For testing, use the example "maize_AC145224.fa"

Specify the directory containing the tallymer index 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/".

Specify the root name of the tallymer index, for example "maize_BACS100_20mer_minocc5".

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below

  • Default parameters only, no further configuration needed.

Output File(s)

Expect a txt file named "tallymer_search_out.txt".  For details on format of the output file please see:

http://www.zbh.uni-hamburg.de/fileadmin/gi/tallymer/tallymer.pdf

Tool Source for App

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