This is the fasta_stats program that is included with the Meraculous genome assembly software. I am not sure of who the original author of this software is.
Install using a typical git clone, then make routine.
git clone https://github.com/conchoecia/fasta_stats.git
cd fasta_stats
make
Then, open either the ~/.bash_profile file or ~/.bashrc file, or however you add new programs to your path,
then add the program to your path like so. Change the absolute path to match wherever your files are saved.
PATH=$PATH:/path/to/fasta_stats/bin
export PATH
Restart your terminal (or close your SSH, then login again), and you should be able to run the program.
Simply run the following command to get stats about a fasta file, typically a genome assembly.
fasta_stats genome_assembly_of_interest.fa
The output will look like this. Keep in mind that N/L50 are accidentally swapped. This is a bug in the software that I have not yet fixed.
Main genome scaffold total: 45
Main genome contig total: 352
Main genome scaffold sequence total: 110.7 MB
Main genome contig sequence total: 110.7 MB (-> 0.0% gap)
Main genome scaffold N/L50: 6/8.5 MB
Main genome contig N/L50: 61/580.4 KB
Number of scaffolds > 50 KB: 13
% main genome in scaffolds > 50 KB: 99.5%
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- --------- ------- ----------- ----------- --------
All 45 352 110,691,255 110,660,632 99.97%
1 kb 45 352 110,691,255 110,660,632 99.97%
2.5 kb 45 352 110,691,255 110,660,632 99.97%
5 kb 44 351 110,686,898 110,656,275 99.97%
10 kb 36 343 110,629,701 110,599,078 99.97%
25 kb 23 330 110,434,894 110,404,271 99.97%
50 kb 13 319 110,109,091 110,078,568 99.97%
100 kb 13 319 110,109,091 110,078,568 99.97%
250 kb 13 319 110,109,091 110,078,568 99.97%
500 kb 13 319 110,109,091 110,078,568 99.97%
1 mb 13 319 110,109,091 110,078,568 99.97%
2.5 mb 13 319 110,109,091 110,078,568 99.97%
5 mb 13 319 110,109,091 110,078,568 99.97%