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