Download genomes in batch from NCBI
curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)(GCA/)([0-9]{3}/)([0-9]{3}/)([0-9]{3}/)(GCA_.+)|\1\2\3\4\5\6/\6_genomic.fna.gz|' > genomic_file2261 days ago
1760 days ago
Bash script to download SRA file !
...mand ensures we get two files, one for the first and second mate in each pair. We'll use them in this format when aligning. wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra instant/r...1558 days ago
Pack a perl program with their dependencies on Ubuntu !
...dump files !By Jit 37 days ago extracttaxdumpreadmetaxonomyncbi This is an extract of taxdump-readme.txt to be found at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ R...1510 days ago
1440 days ago
Sequence Ids conversion files !
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ Name Size Date Modified ARCHIVE/ 02/.../ 18/04/2020, 00:15:00 737 B 09/06/2011, 05:30:00 ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ac...1401 days ago
Parse the NCBI taxonomy database with Perl !
use Bio::DB::Taxonomy; use warnings; my $sps="human"; # Get one from a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile',...1171 days ago
Perl script to get all the descendent in a tree !
use warnings; use Bio::DB::Taxonomy; #Rotifera 10190 # Get one from a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile',...1163 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...Downloading third party database for Alienomics\n"; #Install NCBI taxdump my $url = 'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxd...wnload my $result = `mkdir taxdump; cd taxdump; wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxd...1159 days ago
1157 days ago