The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

 

 

 

 

 

Skip to end of metadata
Go to start of metadata

Suffixerator

Community rating: ?????

Suffixerator builds an enhanced suffix array (ESA) from one or more fasta sequence files. The ESA data structure provides a flexible and memory-efficient way of counting k-mers using Tallymer tools.

Quick Start

Test Data

Icon

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)

Use maize_BAC100.fa from the directory above as test input.  This file contains 100 finished maize BACs described in Haberer et al. Plant Physiol. 2005 Dec;139(4):1612-24.

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.

  • Use these parameters within the DE app interface:
    • Input fasta -- Add one or more fasta sequence files.  Each fasta file may have multiple sequences.
    • ESA name (default "my_esa"): Give your enhanced suffix array a root name of your choosing.  Otherwise the default name of "my_esa" will be used

Output File(s)

Suffixerator will generate 9 output files that together constitute the ESA.  For example if you had entered "maize_BAC100" as the desired ESA name the following output files would be generated.

maize_BAC100.al1
maize_BAC100.des
maize_BAC100.esq
maize_BAC100.lcp
maize_BAC100.llv
maize_BAC100.prj
maize_BAC100.sds
maize_BAC100.ssp
maize_BAC100.suf

The above files are available in the Tallymer example_data directory.

Tool Source for App

  • No labels

1 Comment

  1. ★★★★★ Great for making suffix arrays (by bhurwitz)