Question: Creating database in LAST tool with NCBI nt database
0
gravatar for dymphan.17phd
5 weeks ago by
dymphan.17phd0 wrote:

I have installed LAST tool to align nanopore reads. lastdb option is used to create database from fasta file for alignment. For metagenomic study, I need to align my nanopore reads to the NCBI nt (nucleotide) or nr (protein) database. How can I make a database for alignment using LAST tool from (NCBI nt or nr database) which is not in fasta format? Please help.

ADD COMMENTlink modified 5 weeks ago by genomax75k • written 5 weeks ago by dymphan.17phd0

Can you give us some more insight in what exactly you try to achieve? It could be that LAST might not be the appropriate tool for it.

ADD REPLYlink written 5 weeks ago by lieven.sterck6.4k

I want to align the nucleotide bases to the database for classification of microbes present.

ADD REPLYlink written 29 days ago by dymphan.17phd0
0
gravatar for genomax
5 weeks ago by
genomax75k
United States
genomax75k wrote:

You can find nt and nr data files in fasta format in this NCBI directory. These are large downloads but you already know that.

ADD COMMENTlink written 5 weeks ago by genomax75k

Thank you for the information.

ADD REPLYlink written 5 weeks ago by dymphan.17phd0

These are not indexed. Do these sequences need to be indexed in order to see the results. If so how can it be done.

ADD REPLYlink written 5 weeks ago by dymphan.17phd0

that is correct. What genomax pointed you to is the plain fasta files. From here you can download the preformatted ones.

It's also possible to download the fasta files and format them locally. Check the manual of blast and look for the makeblastdb command

EDIT: too quick in answering, what I mentioned above is to format the fasta files for use with ncbi blast not LAST. To format fasta files for LAST you will have to use the lastdb command en give the fasta files you downloaded as input

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by lieven.sterck6.4k

LAST is not the right program to align nanopore data to something as large as nt/nr.

You may want to try kraken2 (https://ccb.jhu.edu/software/kraken2/ ). Keep this recommendation in mind. There are pre-made kraken2 databases that may suffice.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by genomax75k

Thank you for the information.

ADD REPLYlink written 29 days ago by dymphan.17phd0
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