List of bioinformatics packages for NGS analysis !
...thon, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access t...1144 days ago
Useful links to therapy, disease, drug and drug-target network data:
...uctures http://scientific.thomson.com/products/iddb/HOMIM: a knowledgebase of human genes and genetic disorders http://www.ncbi.nlm.nih.gov/ sites/entrez?db=omim PDTD: 3D drug targe...1436 days ago
Entrez Direct: E-utilities on the UNIX Command Line
Entrez Direct (EDirect) is an advanced method for accessing the NCBI's suite of inter...ties or scripts to perform actions that cannot be accomplished entirely within Entrez.2757 days ago
NCBI Prokaryotic Genome Annotation Pipeline
NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). Genome annotation is a multi-level proce...2548 days ago
3949 days ago
Commercial and public next-gen-seq (NGS) software
Integrated solutions CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq softwar...3521 days ago
Python script to download covid genome !
...k-sequences'] print("got %d sequences" % len(seqs)) from Bio import Entrez allseq = {} for x in seqs:...ete": nm = x['accession'] print("downloading", nm) dna = Entrez.efetch(db='nucleotide',id=nm,...1138 days ago
Install NCBI entrez-direct and esearch using conda !
$ conda install -c bioconda entrez-direct Collecting package metadata (current_repodata.json): done Solv...be0_2 Proceed ([y]/n)? y Downloading and Extracting Packages entrez-direct-13.9 | 5.2 MB | #...1103 days ago
Download mutliple fasta file from NCBI in one GO!!
if you have less time, then use three ways mentioned in bookmark link to extract/download all fasta sequences in single click given that you already have a list of GIs or accession IDs . Alternatively, use one liner perl script: perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @A...Tags: fasta, multiple fasta, ncbi, entrez, perl
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Comment on "List of gene ontology software and tools"
GeneSCF serves as command line tool for clustering list of genes based on functional annotation (Geneontology, KEGG, REACTOME and NCG). This tool requires gene list in the form of Entrez Gene IDs or Official gene symbols as a input. http://genescf.kandurilab.org/1494 days ago
Comment on "SPAdes hybrid genome assembly"
...38 > single_contig.fa Finally, a quick comparison to the reference: sudo apt-get install mummer curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleot...2176 days ago