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. 

Header

Description

count

Count of sequences in fasta file

sum_len

Total length of sequences

N50

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

min_len

Length of shortest sequence

max_len

Length of longest sequence

med_len

Median length of sequences

ave_len

Mean length of sequences

sd_len

Standard deviation of the mean

file

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

Tool Source for App

  • Not applicable