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Contents of README: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 |
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Parent Directory - README 03-Jun-2022 18:26 1.3K References 03-Jun-2022 18:26 139 diamond-0.9.36.tar.gz 04-Jun-2022 01:48 1.1M diamond.SlackBuild 11-Mar-2022 06:34 3.2K diamond.info 03-Jun-2022 18:26 313 slack-desc 03-Jun-2022 18:26 936
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