Question: All completed genomes for a phyla
0
gravatar for frenchmytoast112
3.3 years ago by
frenchmytoast11210 wrote:

Hello everyone,

is it possible to find all the completed genomes for certain phyla by obtaining their accession number?
I found some questions and answer here about it, but they all seem outdated or unclear. For example, I would like to access all the genomes for Acidobacteria from NCBI, which are finished and completed.

genome • 1.1k views
ADD COMMENTlink modified 3.3 years ago by Erik Wright350 • written 3.3 years ago by frenchmytoast11210
2

I just used NCBI Taxonomy Database to see all sequence data for Acidobacteria (see: here). To access the list of all genomes for this phylum, click on the Assembly link.

ADD REPLYlink written 3.3 years ago by a.zielezinski8.6k

Thats Assembly. Are they completed genomes? I am not sure thats what I was asking for.

ADD REPLYlink written 3.3 years ago by frenchmytoast11210
5
gravatar for Erik Wright
3.3 years ago by
Erik Wright350
Erik Wright350 wrote:

NCBI has a list of genomes by organism.  Enter "Acidobacteria" then click "Search by organism".  Next, select the prokaryotes tab.  Sort by the "Level" column.  Completed genomes have a filled black circle.

If the list is too long to click each genome individually, there is a link near the top that says "Download selected records".  This produces a file with multiple columns, including the RefSeq ftp directory address.  Simply write a script to download the file(s) that you want from each of those directories.

For example, the R script I use for downloading the FASTA files looks like this:

# read in the file downloaded from the NCBI genome browser
x <- read.csv("<<PATH TO genomes_proks.csv>>", stringsAsFactors=FALSE)
ftps <- x$GenBank.FTP

# select a subset of FTPs if desired
ftps <- ftps[which(x$Level=="Complete Genome")]

# set the input and output file locations
ftps <- paste(ftps,
    paste0(sapply(strsplit(ftps, "/", fixed=TRUE), tail, n=1),
        "_genomic.fna.gz"),
    sep="/")
saveto <- paste0("~/Downloads/",
    sapply(strsplit(ftps, "/", fixed=TRUE), tail, n=1))

# download each of the genomes to ~/Downloads/
pBar <- txtProgressBar(style=3)
for (i in seq_along(ftps)) {
    download.file(ftps[i], saveto[i])
    setTxtProgressBar(pBar, i/length(ftps))
}

Hope that helps!

ADD COMMENTlink written 3.3 years ago by Erik Wright350

Thats it! Thanks!
But how did you learn about this? I am a bit confused about NCBI and its ins and outs.

ADD REPLYlink written 3.3 years ago by frenchmytoast11210
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