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Repository diamond
Name: diamond
Owner: bgruening
Synopsis: DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500 times faster than BLASTX, finding more than 94% of all matches. http://ab.inf.uni-tuebingen.de/software/diamond/
Content homepage: https://github.com/bbuchfink/diamond
Development repository: https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond
Link to this repository: https://toolshed.g2.bx.psu.edu/view/bgruening/diamond/a02aa0dfb850
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/diamond
Type: unrestricted
Revision: 18:a02aa0dfb850
This revision can be installed: True
Times cloned / installed: 3249

Repository README files - may contain important installation or license information

Readme files
BLAST DBs come with additional taxonomic data: taxdb.btd, taxdb.bti, taxonomy4blast.sqlite3
which are quite large. this folder contains small test data covering a few species

Oryza sativa    4530
Drosophila      7215
Danio rerio     7955
Homo sapiens    9606
Mus musculus    10090

the files have been provided to @bernt-matthias by the NCBI help desk (ticket help #247163)

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
align sequences against a protein database 2.1.22+galaxy0 24.1
build database from a FASTA file 2.1.22+galaxy0 23.2
generate formatted output from DAA files 2.1.22+galaxy0 23.2

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis