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33 lines
1.3 KiB
Text
33 lines
1.3 KiB
Text
DIAMOND is a sequence aligner for protein and translated DNA searches,
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designed for high performance analysis of big sequence data. The key
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features are:
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- Pairwise alignment of proteins and translated DNA at 500x-20,000x
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speed of BLAST.
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- Frameshift alignments for long read analysis.
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- Low resource requirements and suitable for running on standard
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desktops or laptops.
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- Various output formats, including BLAST pairwise, tabular and XML,
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as well as taxonomic classification.
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To now run an alignment task, we assume to have a protein database file
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in FASTA format named 'nr.faa' and a file of DNA reads that we want to
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align named 'reads.fna'.
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In order to set up a reference database for DIAMOND, the 'makedb'
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command needs to be executed with the following command line:
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$ diamond makedb --in nr.faa -d nr
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This will create a binary DIAMOND database file with the specified name
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('nr.dmnd'). The alignment task may then be initiated using the 'blastx'
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command like this:
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$ diamond blastx -d nr -q reads.fna -o matches.m8
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The output file here is specified with the '-o' option and named
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'matches.m8'. By default, it is generated in BLAST tabular format.
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Publication:
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Buchfink B, Xie C, Huson DH, "Fast and sensitive protein alignment using
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DIAMOND", Nature Methods 12, 59-60 (2015). doi:10.1038/nmeth.3176
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