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Diffstat (limited to 'academic/diamond/README')
| -rw-r--r-- | academic/diamond/README | 12 |
1 files changed, 6 insertions, 6 deletions
diff --git a/academic/diamond/README b/academic/diamond/README index a5c66d0988923..07af60110e715 100644 --- a/academic/diamond/README +++ b/academic/diamond/README @@ -11,22 +11,22 @@ features are: 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 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` +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` +('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. +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 |