Results for "ncbi"
Bio-Scripts
(JitMetaENV) ➜ JitMeta conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1208 days ago
Python script to download covid genome !
...s://www.gisaid.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/genba...1127 days ago
Install NCBI entrez-direct and esearch using conda !
$ conda install -c bioconda entrez-direct Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of co...1092 days ago
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -que...1092 days ago
Install BLAST in Ubuntu/Linux and Window !
#On ubuntu sudo apt-get install ncbi-blast+ #Ubuntu Conda installation...nstallation First: Download ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-win64.exe with y...should put BLAST under C:\Program Files\NCBI\blast-2.7.1+1138 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings...at => undef, verbose => undef, url => 'http://www.ncbi.nlm.nih.gov/entrez/eutils',...2907 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed under GNU General Public License. # This script will parse a NCBI blastx output file and output the to...2905 days ago
Download the genome from NCBI using bash script/command
...# -for fungi curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fu...$20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(...-for plant curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/pl...$20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(...2523 days ago
Download the gff files from NCBI using bash script/command
...# -for fungi curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fu...$20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(...$20} ' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(...ebrate_other curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/ve...2514 days ago
Loop over with all files in a directory in bash
#!/bin/bash FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/* ref=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/GCA_000196735.1_ASM19673v1_genomic.fna path=/home/urbe/Tools/SATSUMA/satsuma-code-...2322 days ago
