RefSoil

This repository provide the list of reference soil. (RefSoil_v1.txt)

RefSoil_v1.txt

Each colume represents: uniq ID, chromosomes, version, taxon ID, Definition, Organism, Full taxonomy

RefSoil version 1 contains 928 genomes (888 bacteria, 34 archaea, 6 fungi) and 1070 chromosomes

How to download RefSoil database

Download from figshare

Probably the easiest way is the go to the following link to download file https://figshare.com/articles/RefSoil_Database/4362812

Download using script

You can also download from NCBI using list of ID and given script bellow.

First, clone this repository

git clone https://github.com/germs-lab/ref_soil.git

Download Genbank format

python script_download_refsoil/fetch_genbank.py script_download_refsoil/refsoil_id.txt refsoil_genbank

Download full genome nucleotide sequence in FASTA format

python script_download_refsoil/fetch_fasta_genome.py script_download_refsoil/refsoil_id.txt refsoil_full_genome_fasta

Download CDS nucleotide in FASTA format

python script_download_refsoil/fetch_fasta_cds.py script_download_refsoil/refsoil_id.txt refsoil_cds_fasta

Download protein sequence in FASTA format

python script_download_refsoil/fetch_fasta_protein.py script_download_refsoil/refsoil_id.txt refsoil_protein_fasta

Download single cell genome

NCBI ID of single cell genomes are in the file "sc_id.txt". You can use same script above with the ID-file

python script_download_refsoil/fetch_genbank.py script_download_refsoil/sc_id.txt single_cell_genome

List of the script

Get 16s rRNA gene sequences

Build 16s rRNA gene tree

RAST analysis

Compare RefSeq