Results for "NIH"
Bio-Scripts
Python script to download covid genome !
...isaid.org/ has more (1200?), but they require you to sign up import requests import yaml seqs = yaml.load(requests.get("https://www.ncbi.nlm.nih.gov/core/assets/genbank/files...1130 days ago
Install BLAST in Ubuntu/Linux and Window !
...onda blast #Windows installation First: Download ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/...#If that FTP links does not work, try HTTP instead http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/...1141 days ago
Retrieve NCBI GenBank records with a range of accession numbers
...ef, returnType => undef, maxRecords => undef, format => undef, verbose => undef, url => 'http://www.ncbi.nlm.nih.gov/entrez/eutils', retr...2910 days ago
Download the genome from NCBI using bash script/command
...for fungi curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/asse...} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|...or plant curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/asse...} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|...2526 days ago
Download the gff files from NCBI using bash script/command
...for fungi curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/asse...} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|...or plant curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/asse...} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|...2517 days ago
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_file2257 days ago
- Download page https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download...ast+ CentOS # download latest BLAST version wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/...
1756 days ago
Bash script to download SRA file !
...res 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/reads/ByR...1553 days ago
Pack a perl program with their dependencies on Ubuntu !
...!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/ Rahul...1505 days ago
Sequence Ids conversion files !
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ Name Size Date Modified ARCHIVE/ 02/01/2020...020, 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/gene2accession....1396 days ago
