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


Path to the input protein reference database file in FASTA format (may be gzip compressed).
Path to the output DIAMOND database file.
--threads/-p #
Number of CPU threads. By default, the program will auto-detect and use all available virtual
cores on the machine.
Path to the DIAMOND database file.
Path to the query input file in FASTA or FASTQ format (may be gzip compressed).
--query-gencode #
Genetic code used for translation of query in BLASTX mode. A list of possible values can
be found at the NCBI website. By default, the Standard Code is used.
Path to the output file. If this parameter is omitted, the results will be written to the standard
output and all other program output will be suppressed.
--outfmt/-f #
Format of the output file.
Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed).
This parameter is required when using the staxids field of the BLAST tabular
format. The file can be downloaded from NCBI:
Include full length subject titles into the DAA format. By default, DAA files contain only the
shortened sequence id (up to the first blank character).
--compress (0,1)
Enable compression of the output file. 0 (default) means no compression, 1 means gzip
This mode is a lot more sensitive that the default and generally recommended for aligning
longer sequences. The default mode is mainly designed for short read alignment, i.e. finding
significant matches of >50 bits on 30-40aa fragments.
This mode provides some additional sensitivity compared to the sensitive mode.
--band #
Dynamic programming band for seed extension. This corresponds to the maximum length
of gaps that can be found in alignments.
--gapopen #
Gap open penalty.
--gapextend #
Gap extension penalty.
Scoring matrix.
--comp-based-stats (0,1)
Compositional bias correction of alignment scores. 0 means no score correction, 1 means
compositional bias correction as described in [2] (default). Compositionally biased sequences
often cause false positive matches, which are effectively filtered by this algorithm
in a way similar to the composition based statistics used by BLAST [3].
--seg (yes,no)
Enable SEG masking of low complexity segments in the query. The default is no for blastp
and yes for blastx.
--min-orf/-l #
Ignore translated sequences that do not contain an open reading frame of at least this length.
By default this feature is disabled for sequences of length below 30, set to 20 for sequences
of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature.
--max-target-seqs/-k #
The maximum number of target sequences per query to report alignments for (default=25).
Setting this to 0 will report all alignments that were found.
--top #
Report alignments within the given percentage range of the top alignment score for a query
(overrides --max-target-seqs option).
--evalue/-e #
Maximum expected value to report an alignment (default=0.001).
--min-score #
Minimum bit score to report an alignment. Setting this option will override the --evalue
--id #
Report only alignments above the given percentage of sequence identity.
--query-cover #
Report only alignments above the given percentage of query cover.
--subject-cover #
Report only alignments above the given percentage of subject cover.
--max-hsps #
The maximum number of HSPs per subject sequence to report for each query. By default,
this is set to 1, so only the single best HSP for each query/subject pair will be reported.
--unal (0,1)
Report unaligned queries (0=no, 1=yes). By default, unaligned queries are reported for the
BLAST pairwise, BLAST XML and SAM format.
Suppress reporting of identical self-hits between sequences.
--block-size/-b #
Block size in billions of sequence letters to be processed at a time. This is the main parameter
for controlling the program’s memory usage. Bigger numbers will increase the use
of memory and temporary disk space, but also improve performance. The program can be
expected to use roughly six times this number of memory (in GB). So for the default value of
-b2.0, the memory usage will be about 12 GB.
Directory to be used for temporary storage. This is set to the output directory by default.
The amount of disk space that will be used depends on the program’s settings and your
data. As a general rule you should ensure that 100 GB of disk space are available here.
If you run the program in a cluster environment, and disk space is only available over a
slow network based file system, you may want to set the --tmpdir option to /dev/shm. This
will keep temporary information in memory and thus increase the program’s memory usage
--index-chunks/-c #
The number of chunks for processing the seed index (default=4). This option can be additionally
used to tune the performance. It is recommended to set this to 1 on a high memory
server, which will increase performance and memory usage, but not the usage of temporary
disk space.--daa/-a
Path to input file in DAA format.
Path to output file. If this parameter is omitted, the results will be written to the standard
output and all other program output will be suppressed.
--outfmt/-f #
Format of the output file, see 3.3.
--compress (0,1)
Enable compression of the output file
--freq-sd #
During the seed search, seeds with very high frequency in the queries or the database are
ignored. This option sets the number of standard deviations above the average frequency
for ignoring a seed. The default values are 50 in default mode, 10 in sensitive mode, and
200 in more-sensitive mode.

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