diamond - accelerated BLAST compatible local sequence aligner
diamond COMMAND [OPTIONS]
DIAMOND is a sequence aligner for protein and translated DNA
searches
and functions as a drop-in replacement for the NCBI BLAST software
tools. It is suitable for protein-protein search as well as DNA-protein
search on short reads and longer sequences including contigs and
assemblies, providing a speedup of BLAST ranging up to x20,000.
- makedb
- Build DIAMOND database from a FASTA file
- blastp
- Align amino acid query sequences against a protein reference database
- blastx
- Align DNA query sequences against a protein reference database
- view
- View DIAMOND alignment archive (DAA) formatted file
- help
- Produce help message
- version
- Display version information
- getseq
- Retrieve sequences from a DIAMOND database file
- --threads
(-p)
- number of CPU threads
- --db (-d)
- database file
- --out
(-o)
- output file
- --outfmt
(-f)
- output format
- 0 = BLAST pairwise
- 5 = BLAST XML
- 6 = BLAST tabular
- 100 = DIAMOND alignment archive (DAA)
- 101 = SAM
- Value 6 may be followed by a space-separated list of these keywords:
- qseqid means Query Seq - id
- qlen means Query sequence length
- sseqid means Subject Seq - id
- sallseqid means All subject Seq - id(s), separated by a ';'
- slen means Subject sequence length
- qstart means Start of alignment in query
- qend means End of alignment in query
- sstart means Start of alignment in subject
- send means End of alignment in subject
- qseq means Aligned part of query sequence
- sseq means Aligned part of subject sequence
- evalue means Expect value
- bitscore means Bit score
- score means Raw score
- length means Alignment length
- pident means Percentage of identical matches
- nident means Number of identical matches
- mismatch means Number of mismatches
- positive means Number of positive - scoring matches
- gapopen means Number of gap openings
- gaps means Total number of gaps
- ppos means Percentage of positive - scoring matches
- qframe means Query frame
- btop means Blast traceback operations(BTOP)
- stitle means Subject Title
- salltitles means All Subject Title(s), separated by a '<>'
- qcovhsp means Query Coverage Per HSP
- qtitle means Query title
- Default: qseqid sseqid pident length mismatch gapopen qstart qend sstart
send evalue bitscore
- --verbose
(-v)
- verbose console output
- --log
- enable debug log
- --quiet
- disable console output
- --in
- input reference file in FASTA format
- --seq
- Sequence numbers to display.
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.