raw data origine

Question

[lamlam]

Hello
I have raw data of the sequence fasta format, but I do not know its origin, ie the sample sequenced. Is there software to know the origin of data?????

[GenoMax]

You can possibly identify what organism the data is from by doing a sequence similarity search (e.g.blast @NCBI) but that would not guarantee origin of the sample.

[lamlam]

I have a assembly data with lot of contig but when i use the blast i compare the contug not with data base

[GenoMax]

What database are you comparing it to?

[kamel]

by what tools I know the closest species from assembly result (Fasta)

[GenoMax]

Blast @NCBI would be the easiest option. You would know the exact species if there are sequences from that species in the database.

Answer 1

[michael.ante]

Hi lamlam,

You can use the FastQ screen tool or compute overrepresented sequences and blast them.

Cheers,

Michael

[lamlam]

Can i use FastQ screen on windows?

[michael.ante]

According to the Readme, you can run it under Windows, after installing Bowtie2, Perl, and GD::Graph. In the readme, you'll find suggestions how to install these.

[lamlam]

thank you i will do it