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14.2 > Academic > diamond (0.9.23)

DIAMOND is a sequence aligner for protein and translated DNA searches,
designed for high performance analysis of big sequence data. The key
features are:

- Pairwise alignment of proteins and translated DNA at 500x-20,000x
speed of BLAST.
- Frameshift alignments for long read analysis.
- Low resource requirements and suitable for running on standard
desktops or laptops.
- Various output formats, including BLAST pairwise, tabular and XML,
as well as taxonomic classification.

To now run an alignment task, we assume to have a protein database file
in FASTA format named `nr.faa` and a file of DNA reads that we want to
align named `reads.fna`.

In order to set up a reference database for DIAMOND, the `makedb`
command needs to be executed with the following command line:

$ diamond makedb --in nr.faa -d nr

This will create a binary DIAMOND database file with the specified name
(`nr.dmnd`). The alignment task may then be initiated using the `blastx`
command like this:

$ diamond blastx -d nr -q reads.fna -o matches.m8

The output file here is specified with the `–o` option and named
`matches.m8`. By default, it is generated in BLAST tabular format.

Publication:
Buchfink B, Xie C, Huson DH, "Fast and sensitive protein alignment using
DIAMOND", Nature Methods 12, 59-60 (2015). doi:10.1038/nmeth.3176

Maintained by: Petar Petrov
Keywords: sequence aligner,protein,DNA
ChangeLog: diamond

Homepage:
https://github.com/bbuchfink/diamond

Source Downloads:
diamond-0.9.23.tar.gz (3597695081d4b6fd8978c257cdb5fe4a)

Download SlackBuild:
diamond.tar.gz
diamond.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

Individual Files:
README
References
diamond.SlackBuild
diamond.info
slack-desc

Validated for Slackware 14.2

See our HOWTO for instructions on how to use the contents of this repository.

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