assembly-stats
Get assembly statistics from FASTA and FASTQ files.
Contents
Installation
If you encounter an issue when installing assembly-stats please contact your local system administrator. If you encounter a bug please log it here.
Dependencies
- zlib
Compiling from source
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 files can be supplied in compressed format (.gz, .bz2 or .xz). Compression support depends on what libraries are available when assembly-stats is compiled. Compression type is detected automatically and does not depend on the file name extensions.
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 consecutive run of Ns (undetermined nucleotide bases) of any length (it is case-insensitive so
counts any "n" as well). N_count is the total Ns (undetermined nucleotide bases) across the entire assembly.
License
assembly-stats is free software, licensed under GPLv3.
Feedback/Issues
We currently do not have the resources to provide support for assembly-stats. However, the community might be able to help you out if you report any issues about usage of the software to the issues page.