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

Discovery Environment Applications List

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Compute Contig Statistics

Compute Contig Statistics provides basic statistics relating to the length of sequences within a fasta file.  It takes a single file containing one or more sequences in fasta format as input and returns a text file.

Quick Start

  • To use Compute Contig Statistics, upload your data in fasta format.

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > sequence_statistics

Input File(s)

Use SperuDNc5l100-sample.fa

Parameters Used in App

  • Default parameters only, no further configuration needed.

Output File(s)

Expect a txt file as output. 




Count of sequences in fasta file


Total length of sequences


Sequences of the N50 length and greater together account for 50% of the total length of sequences in the file


Length of shortest sequence


Length of longest sequence


Median length of sequences


Mean length of sequences


Standard deviation of the mean


File name (e.g. SperuDNc5I100-sample.fa)

Tool Source for App

  • Not applicable