How To Download Fasta Sequence From Ncbi
To download all viral RefSeq genomes in FASTA format, run: ncbi-genome-download --format fasta viral. It is possible to download multiple formats by supplying.
- Some Easy Ways to Download Multiple Sequences from NCBI. This is another quick and easy way to download MULTIPLE NCBI sequences in a go. Steps to download sequences by EUtilities. Convert Multi Fasta file into a Single line FASTA File. Bioinformatics resources (56) Bioinformatics Video Tutorial (26).
- Their script to download genomes, ncbi-genome-download. For a quick example here, I’m going to pull fasta files for all RefSeq Alteromonas reference genomes labeled as “complete” – see here for definitions of RefSeq. Here’s the syntax to pull a single protein sequence: ncbi-acc-download -m protein WP.
How do download multiple fasta sequences from NCBI all at once? For example, I received these accession numbers: DQ860511–DQ860642 from a research article and would like to download them all at. Please download and install the following software: 1. Using BLAST, we will download sequences from GenBank in both FASTA and GenBank. FASTA (pronounced FAST-AYE) is a suite of programs for searching nucleotide or protein databases with a query sequence. FASTA itself performs a local heuristic search of a protein or nucleotide database for a query of the same type. FASTX and FASTY translate a nucleotide query for searching a protein database. TFASTX and TFASTY translate a nucleotide database to be searched with a protein query.
Some script to download bacterial and fungal genomes from NCBI after theyrestructured their FTP a while ago.
Idea shamelessly stolen from Mick Watson's Kraken downloaderscriptsthat can also be found in Mick's GitHubrepo. However, Mick'sscripts are written in Perl specific to actually building a Kraken database(as advertised).
So this is a set of scripts that focuses on the actual genome downloading.
Installation
Alternatively, clone this repository from GitHub, then run (in a python virtual environment)
If this fails on older versions of Python, try updating your pip tool first:
and then rerun the ncbi-genome-download install.
Alternatively, ncbi-genome-download is packaged in conda.Refer the the Anaconda/miniconda site to install a distribution (highly recommended) https://conda.io/miniconda.htmlWith that installed one can do:
ncbi-genome-download is only developed and tested on Python releases still under activesupport by the Python project. At the moment, this means versions 2.7, 3.4, 3.5 and 3.6.Specifically, no attempt at testing under Python versions older than 2.7 or 3.4 is being made.
If your system is stuck on an older version of Python, consider using a tool likeHomebrew or Linuxbrew to obtain a more up-to-dateversion.
Usage
To download all bacterial RefSeq genomes in GenBank format from NCBI, run the following:
Downloading multiple groups is also possible:
If you're on a reasonably fast connection, you might want to try running multiple downloads in parallel:
To download all fungal GenBank genomes from NCBI in GenBank format, run:
To download all viral RefSeq genomes in FASTA format, run:
It is possible to download multiple formats by supplying a list of formats or simply download all formats:
To download only completed bacterial RefSeq genomes in GenBank format, run:
It is possible to download multiple assembly levels at once by supplying a list:
To download only bacterial reference genomes from RefSeq in GenBank format, run:
To download bacterial RefSeq genomes of the genus Streptomyces, run:
Note: This is a simple string match on the organism name provided by NCBI only.
You can also use this with a slight trick to download genomes of a certain species as well:
Note: The quotes are important. Again, this is a simple string match on the organismname provided by the NCBI.
Multiple genera is also possible:
You can also put genus names into a file, one organism per line, e.g.:
Fasta Database
Then, pass the path to that file (e.g. my_genera.txt) to the --genus option, like so:
Note: The above command will download all Streptomyces and Amycolatopsis genomes from RefSeq.
You can make the string match fuzzy using the --fuzzy-genus option. This can be handy if you need to matcha value in the middle of the NCBI organism name, like so:
Note: The above command will download all bacterial genomes containing 'coelicolor' anywhere in theirorganism name from RefSeq.
To download bacterial RefSeq genomes based on their NCBI species taxonomy ID, run:
Note: The above command will download all RefSeq genomes belonging to Escherichia coli.
To download a specific bacterial RefSeq genomes based on its NCBI taxonomy ID, run:
Note: The above command will download the RefSeq genome belonging to Escherichia coli str. K-12 substr. MG1655.
It is also possible to download multiple species taxids or taxids by supplying the numbers in a comma-separated list:
Note: The above command will download the reference genomes for cat and human.
In addition, you can put multiple species taxids or taxids into a file, one per lineand pass that filename to the --species-taxid or --taxid parameters, respectively.
Pfam
Assuming you had a file my_taxids.txt with the following contents:
You could download the reference genomes for cat and human like this:
It is possible to also create a human-readable directory structure in parallel to mirroringthe layout used by NCBI:
This will use links to point to the appropriate files in the NCBI directory structure,so it saves file space. Note that links are not supported on some Windows file systems and someolder versions of Windows.
It is also possible to re-run a previous download with the --human-readable option.In this case, ncbi-genome-download will not download any new genome files, and just createhuman-readable directory structure. Note that if any files have been changed on the NCBI side,a file download will be triggered.
There is a 'dry-run' option to show which accessions would be downloaded, given your filters:
If you want to filter for the 'relation to type material' column of theassembly summary file, you can use the --type-material option. Possiblevalues are 'any', 'all', 'type', 'reference', 'synonym', 'proxytype', and/or'neotype'. 'any' will include assemblies with no relation to type materialvalue defined, 'all' will download only assemblies with a defined value.Multiple values can be given, separated by comma:
By default, ncbi-genome-download caches the assembly summary files for the respective taxonomicgroups for one day. You can skip using the cache file by using the --no-cache option.The output of --help also shows the cache directory, should you want to remove any of the cachedfiles.
To get an overview of all options, run
As a method
You can also use it as a method call. Pass the pythonised keyword arguments (_ instead of -)as described above or in the --help:
Note: To specify a taxonomic group, like bacteria, use the group keyword.
Contributed Scripts: gimme_taxa.py
This script lets you find out what TaxIDs to pass to ngd, and will write a simple one-item-per-linefile to pass in to it. It utilises the ete3 toolkit, so refer to their site to install the dependencyif it's not already satisfied.
You can query the database using a particular TaxID, or a scientific name. The primary function of thescript is to return all the child taxa of the specified parent taxa. The script has various optionsfor what information is written in the output.
A basic invocation may look like:
Fasta Sequence Example
On first use, a small sqlite database will be created in your home directoryby default (change the location with the --database flag). You can update this databaseby using the --update flag. Note that if the database is not in your home directory,you must specify it with --database or a new database will be created in your homedirectory.
To see all help:
License
Human Genome Fasta File
All code is available under the Apache License version 2, see theLICENSE file for details.