General options:¶

--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

Makedb options:¶

--in

input reference file in FASTA format

Aligner options:¶

--query (-q)

input query file

--un

file for unaligned queries

--unal

report unaligned queries (0=no, 1=yes)

--max-target-seqs (-k)

maximum number of target sequences to report alignments for

--top

report alignments within this percentage range of top alignment score (overrides --max-target-seqs)

--compress

compression for output files (0=none, 1=gzip)

--evalue (-e)

maximum e-value to report alignments

--min-score

minimum bit score to report alignments (overrides e-value setting)

--id

minimum identity% to report an alignment

--query-cover

minimum query cover% to report an alignment

--subject-cover

minimum subject cover% to report an alignment

--sensitive

enable sensitive mode (default: fast)

--more-sensitive

enable more sensitive mode (default: fast)

--block-size (-b)

sequence block size in billions of letters (default=2.0)

--index-chunks (-c)

number of chunks for index processing

--tmpdir (-t)

directory for temporary files

--gapopen

gap open penalty (default=11 for protein)

--gapextend

gap extension penalty (default=1 for protein)

--matrix

score matrix for protein alignment (default=BLOSUM62)

--custom-matrix

file containing custom scoring matrix

--lambda

lambda parameter for custom matrix

--K

K parameter for custom matrix

--comp-based-stats

enable composition based statistics (0/1=default)

--seg

enable SEG masking of queries (yes/no)

--query-gencode

genetic code to use to translate query (see user manual)

--salltitles

print full subject titles in output files

--no-self-hits

suppress reporting of identical self hits

Advanced options:¶

--min-orf (-l)

ignore translated sequences without an open reading frame of at least this length

--freq-sd

number of standard deviations for ignoring frequent seeds

--id2

minimum number of identities for stage 1 hit

--window (-w)

window size for local hit search

--xdrop (-x)

xdrop for ungapped alignment

--ungapped-score

minimum alignment score to continue local extension

--hit-band

band for hit verification

--hit-score

minimum score to keep a tentative alignment

--gapped-xdrop (-X)

xdrop for gapped alignment in bits

--band

band for dynamic programming computation

--shapes (-s)

number of seed shapes (0 = all available)

--shape-mask

seed shapes

--index-mode

index mode (0=4x12, 1=16x9)

--fetch-size

trace point fetch size

--rank-factor

include subjects within this range of max-target-seqs

--rank-ratio

include subjects within this ratio of last hit

--max-hsps

maximum number of HSPs per subject sequence to save for each query

--dbsize

effective database size (in letters)

--no-auto-append

disable auto appending of DAA and DMND file extensions

--target-fetch-size

number of target sequences to fetch for seed extension

View options¶

--daa (-a)

DIAMOND alignment archive (DAA) file

--forwardonly

only show alignments of forward strand

Getseq options¶

--seq

Sequence numbers to display.