Creating database in LAST tool with NCBI nt database

Question

[dymphan.17phd]

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.

[lieven.sterck]

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.

[dymphan.17phd]

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

Answer 1

[GenoMax]

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

[dymphan.17phd]

Thank you for the information.

[dymphan.17phd]

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

[lieven.sterck]

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

[GenoMax]

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.

[dymphan.17phd]

Thank you for the information.