From 673d7a7bca57ec13a9e8205932e33c8dbbdc9d80 Mon Sep 17 00:00:00 2001 From: Patrick Durand Date: Wed, 10 Nov 2021 10:29:32 +0100 Subject: [PATCH] update README --- README.md | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 1302960..1504553 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,22 @@ # *BeeDeeM*: the Bioinformatics Databank Manager System -[![License AGPL](https://img.shields.io/badge/license-Affero%20GPL%203.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.txt) [![Build Status](https://travis-ci.org/pgdurand/BeeDeeM.svg?branch=master)](https://travis-ci.org/pgdurand/BeeDeeM) [![](https://tokei.rs/b1/github/pgdurand/BeeDeeM?category=code)](https://github.com/pgdurand/BeeDeeM) [![](https://img.shields.io/badge/platform-Java--1.8+-yellow.svg)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) [![](https://img.shields.io/badge/run_on-Linux--macOS--Windows-yellowgreen.svg)]() +[![License AGPL](https://img.shields.io/badge/license-Affero%20GPL%203.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.txt) [![](https://tokei.rs/b1/github/pgdurand/BeeDeeM?category=code)](https://github.com/pgdurand/BeeDeeM) [![](https://img.shields.io/badge/platform-Java--1.8+-yellow.svg)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) [![](https://img.shields.io/badge/run_on-Linux--macOS--Windows-yellowgreen.svg)]() *BeeDeeM* is a general purpose **B**ioinformatics **D**atabank **M**anager. -It provides a suite of command-line and UI softwares to install and use major sequence databanks and biological classifications. It is the ideal companion of the [NCBI BLAST suite of softwares](https://pgdurand.gitbooks.io/beedeem/test_install.html#run-a-blast-search) and [PLAST](https://plast.inria.fr/). +It provides a suite of command-line and UI softwares to install and use major sequence databanks and biological classifications. It is the ideal companion of the [NCBI BLAST suite of softwares](https://pgdurand.gitbooks.io/beedeem/test_install.html#run-a-blast-search) and [PLAST](https://plast.inria.fr/), as well as tools such as [ORSON](https://github.com/ifremer-bioinformatics/orson) annotation pipeline, [BLAST Viewer](https://github.com/pgdurand/BlastViewer) platform. ## Main features *BeeDeeM* automatically performs: -* the download of the database files from remote sites \(via FTP, Aspera\), +* the download of the database files from remote sites \(via FTP, HTTP or Aspera\), * the decompression of the files \(gzip files\), * the un-archiving of the files \(tar files\), * the conversion of native sequence banks \(e.g. Genbank\) to FASTA files, * the preparation of databases in BLAST format from native sequence bank formats, +° the preparation of other indexes such as Diamond, Bowtie, Hisat, etc. * the indexing of Genbank, Refseq, Embl, Genpept, Swissprot, TrEmbl and Fasta files allowing their efficient querying by way of sequence identifiers, * the indexing of sequence features and ontologies data (NCBI Taxonomy, Gene Ontology, Enzyme Commission, Intepro domains and PFAM domains), * the preparation of taxonomic subsets out of annotated sequence banks, @@ -47,7 +48,7 @@ Here is an example of a script to start Genbank_CoreNucleotide installation on I # Release of BeeDeeM to use BDM_HOME="$SOFT/bioinfo/beedeem" -BDM_VER="5.5.1" +BDM_VER="4.7.1" # Load BeeDeeM environment module load java/1.8.0_121 @@ -73,8 +74,8 @@ Here is a screenshot of BeeDeeM user friendly interface: Among others, these databanks can be used to: * prepare and maintain up-to-date local copy of usefull data -* run BLAST sequence comparison jobs -* annotate BLAST results with sequence features and ontologies +* run BLAST, Diamond or PLAST sequence comparison jobs +* annotate BLAST, Diamond or PLAST results with sequence features and ontologies ## Companion tools