Get assembly statistics from FASTA and FASTQ files.
Run the following commands to install the program
mkdir build cd build cmake .. make make test make install
If you do not have root access, you can install to a directory of your choice by changing the call to cmake. For example:
cmake -DINSTALL_DIR:PATH=/foo/bar/ ..
would mean you finish up with a copy of
assembly-stats in the directory
Get statistics from a list of files:
assembly-stats file.fasta another_file.fastq
Detection of FASTA or FASTQ format of each file is automatic from the file contents, so file names and extensions are irrelevant.
The default output format is human readable. You can change the output format and ignore sequences shorter than a given length. Get the full usage by running with no files listed:
$ assembly-stats usage: stats [options] <list of fasta/q files> Reports sequence length statistics from fasta and/or fastq files options: -l <int> Minimum length cutoff for each sequence. Sequences shorter than the cutoff will be ignored  -s Print 'grep friendly' output -t Print tab-delimited output -u Print tab-delimited output with no header line
Here is an example on the Plasmodium falciparum reference genome:
$ assembly-stats Pf3D7_v3.fasta stats for Pf3D7_v3.fasta sum = 23328019, n = 16, ave = 1458001.19, largest = 3291936 N50 = 1687656, n = 5 N60 = 1472805, n = 7 N70 = 1445207, n = 8 N80 = 1343557, n = 10 N90 = 1067971, n = 12 N100 = 5967, n = 16 N_count = 0 Gaps = 0
The numbers should be self-explanatory, except maybe lines like
N50 = 1687656, n = 5. The N50 is 1687656, with 50% of the assembly in 5
sequences. A "gap" is any run of Ns of any length (it is case-insensitive so
counts any "n" as well).
assembly-stats is free software, licensed under GPLv3.