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raw data origine

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?????

sequencing next-gen blast alignment
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updated by kamel • kamel • written by lamlam • lamlam

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.

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written by GenoMax GenoMax

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

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written by lamlam • lamlam

What database are you comparing it to?

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written by GenoMax GenoMax

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

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written by kamel • kamel

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

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written by GenoMax GenoMax

1 answer

Hi lamlam,

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

Cheers,

Michael

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written by michael.ante michael.ante

Can i use FastQ screen on windows?

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written by lamlam • lamlam

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.

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written by michael.ante michael.ante

thank you i will do it

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written by lamlam • lamlam

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