Compute Contig Statistics
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