List of bioinformatics packages for NGS analysis !
Package suites gather software packages and installation tools for specific languages or platforms. We have some for bioinformatics software. Bioconductor &ndas...1105 days ago
Useful links to therapy, disease, drug and drug-target network data:
Useful links to therapy, disease, drug and drug-target network data: DrugBank: a bioinformatics- cheminformatics resource combining detailed drug data with comprehens...1396 days ago
Entrez Direct: E-utilities on the UNIX Command Line
...Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.2718 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...2508 days ago
3910 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...3481 days ago
Python script to download covid genome !
...{} for x in seqs: if 'gene-region' in x and x['gene-region'] == "complete": nm = x['accession'] print("downloading", nm) dna = Entrez.efetch(db='nucleotide',id=nm,...1099 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 con...1064 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 interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined t...Tags: Bioinformatics, Entrez Direct, EDirect, NCBI, Databases, Functions, EDirect, XML, Format, Queries, EDirect, UNIX, Entrez.
2718 days ago
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/1455 days ago
Comment on "SPAdes hybrid genome assembly"
use SPAdes to assemble the data. SPAdes is a swiss-army knife of genome assembly tools, and by default includes read correction. This takes up lots of...2137 days ago