dkj / assembly-stats

Get assembly statistics from FASTA and FASTQ files

assembly-stats

Get assembly statistics from FASTA and FASTQ files.

Installation

Run the following commands to install the program assembly-stats to /usr/local/bin/.

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 /foo/bar/.

Usage

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 [1]
-s
    Print 'grep friendly' output
-t
    Print tab-delimited output
-u
    Print tab-delimited output with no header line

Example

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).