by what tools I know the closest species from assembly result (Fasta)
I have a sequence of mycobacteria but I had not known what species belongs and I am the de novo assembly of several tools and I find a size 7mb blastn and I used to know the closest species but since the size is large blastn does not accept this size. Is that you can help me to know the species closest to that sequence. Thank you
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You can use kraken for this.
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About database integration kraken .is the need to integrate all databases bacteria ??
@gosa: Do use
ADD REPLY/ADD COMMENTbuttons to provide additional information (don't useSUBMIT ANSWERunless you are answering the original question).You can download the database from Kraken site if you don't have the computational resources to do it yourself. It is a ~3GB download.
can you give me the order or the site directly. Thank you
Kraken site https://ccb.jhu.edu/software/kraken/ was linked in my post below. DB is in the downloads section.
I still think you should follow the blast @NCBI option in the post below first.
To explain my problem. I sequenced a bacterial strain unknown and I think it is mycobacterium but I know that strain is Sir can you help me to know what a strain belongs, I novo assembly and I found a size 7Mb.
Have you taken parts (1-2 kb should be enough) of the assembled sequence and just tried to blast them at NCBI (you should not need the whole genome). If your organism is indeed a mycobacterium you should start seeing good hits to mycobacteria (either a specific one or multiple). Depending on what species/strain of mycobacterium shows up in the top hits you could try to download those genomes and then use Mauve to see how similar/co-linear your genome is to those "known" mycobacteria.