How to do genome statistics from fasta and .gz file

[Hani Hasniz]

Hello everyone,

I'm new in this field. Now i have 3 types of files downloaded from public database :
(1) contigs sequence in .gz format
(2) scaffolds sequence in .fasta format
(3) transcriptomes sequence in .fasta format

I don't know what are the steps i should do to get the statistics data (number of scaffolds, N50 count scaffolds, number of contigs, min length of contig, etc). I know i have to run it on linux and maybe using some perl script?

[Brian Bushnell]

Hani,

You can download BBTools and run the included "stats.sh" script. In Linux, the command would be:

stats.sh in=contigs.fasta

But you don't HAVE to run it on Linux, you just need Java installed. In Windows, for example, if you unzip the bbtools package to "C:\bbmap\", the command would be:

java -Xmx200m -cp C:\bbmap\current\ jgi.AssemblyStats2 in=contigs.fasta

The tool works on fasta files whether or not they are gzipped.

[Hani Hasniz]

Hello Brian,

Thank you for the reply. Is BBTools same with BBMap?
Where should i put my .fasta file? in /current/ folder?

[Brian Bushnell]

Yes, BBMap and BBTools are the same package.

You can put the fasta files anywhere, it doesn't matter, as long as you specify a path. For example, if you put a fasta files in /usr/stuff/contigs.fasta, and bbmap is at /usr/programs/bbmap/, then the command would be:

/usr/programs/bbmap/stats.sh in=/usr/stuff/contigs.fasta

[Hani Hasniz]

Hello again,

Why when i'm using stats.sh in=contigs.fasta in Linux, i get :
-bash: stats.sh: command not found ?

[dpryan]

The shell script just isn't in your $PATH.

[Brian Bushnell]

The simplest way to resolve this is to type "./stats.sh", if you are in the same directory, or use the full absolute path otherwise.