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