BlastX

Flag: --add-self-aln

Seed search algorithm (0=double-indexed/1=query-indexed/ctg=contiguous-seed)

File or aligned queries

Format of aligned query file.

Use chaining with extension.

Flag: --aln-out

Flag: --anchored-swipe

Flag: --anchor-score

Flag: --anchor-window

Flag: --ants

Flag: --approx-backtrace

Minimum approximate identity % to report an alignment/to cluster sequences.

Band for dynamic programming computation

Flag: --band-bin

Flag: --bcutoff

Number of query bins for seed search.

Sequence block size in billions of letters.

Flag: --bmatch

Flag: --bmismatch

Flag: --bootstrap

Flag: --bootstrap-block

Flag: --cbs-angle

Flag: --cbs-err-tolerance

Flag: --cbs-it-limit

Flag: --cbs-matrix-scale

Flag: --cbs-window

Flag: --centroid-factor

Flag: --chaining-len-cap

Flag: --chaining-maxgap

Flag: --chaining-maxnodes

Flag: --chaining-min-nodes

Use chaining without extension

Flag: --chaining-range-cover

Flag: --chaining-stacked-hsp-ratio

Scaling factor for the chaining gap penalty.

Scaling factor for the chaining skip penalty.

Flag: --check-multi-target

Flag: --chunk-size-multiplier

Flag: --classic-band

Clustering algorithm ('mcl')

Filename for dumping the graph or reading the graph if cluster-restart.

Restart clustering from dumped graph.

Clustering similarity measure.

Threshold for the similarity measure.

Flag: --col-bin

Composition based statistics mode.

Compression for output files.

Minimum range overlap with higher scoring hit to delete a hit (default=50%)

File containing custom scoring matrix.

Flag: --cut-bar

Flag: --cutoff-score-8bit

DIAMOND alignment archive (DAA) file

Path to the target DIAMOND database file.

Effective database size (in letters).

Type of sequences in database file (nucl/prot).

Flag: --deque_bucket_size

Flag: --d_exp

Flag: --diag-filter-cov

Flag: --diag-filter-id

Flag: --diag-min-estimate

Flag: --d_new

Maximum e-value to report alignments.

Chunk size for adaptive ranking.

Extension algorithm (wfa, ksw=default)

Extension mode.

Flag: --ext-yield

Flag: --family-cap

Flag: --family-counts

Flag: --family-map

File: --family-map-query

Enable fast mode.

Enable faster mode.

Flag: --fast-tsv

Trace point fetch size.

Flag: --file1

Flag: --file2

File buffer size in bytes.

Frame shift penalty (default=disabled)

Mask seeds based on frequency

Number of standard deviations for ignoring frequent seeds.

Flag: --freq-treshold // TYPO: This typo exists in the diamond cli source.

Flag: --full-sw-len

Gap extension penalty.

Gap open penalty.

Flag: --gapped-filter-diag-score

E-value threshold for gapped filter (auto)

Flag: --gapped-filter-evalue1

Flag: --gapped-filter-window

Number of targets for global ranking.

Flag: --graph-algo

Flag: --hamming-ext

Flag: --hard-masked

Flag: --hash_join_swap

Use header lines in tabular output format.

Flag: --heartbeat

Minimum number of identities for stage 1 hit.

Flag: --idl

Flag: --idn

Flag: --idr

Ignore warnings

Include all subject ids in DAA file

Include full subject titles in DAA file.

Include lineage in the taxonomic classification format.

Number of chunks for index processing.

Iterated search with increasing sensitivity.

Flag: --join-ht-factor

Flag: --join-split-key-len

Flag: --join-split-size

Flag: --key2

Flag: --left-most-interval

Flag: --length-ratio-threshold

Only consider seed hits against longest target for identical seeds.

Only consider seed hits against longest query for identical seeds.

Flag: --load-balancing

Enable even more verbose terminal output, which is also written to a file named diamond.log is the current working directory.

Flag: --log-evalue-scale

Flag: --log-extend

Flag: --log-query

Flag: --log-subject

Short for --range-culling --top 10 -F 15.

Flag: --mapany

Masking algorithm.

Score matrix for protein alignment.

Flag: --max-cells

Maximum number of HSPs per target sequence to report for each query.

Maximum seed frequency.

Flag: --max-indirection

Flag: --max-motif-len

Flag: --max-swipe-dp

Maximum number of target sequences to report alignments for.

MCL chunk size per thread.

MCL expansion coefficient.

MCL inflation coefficient.

MCL maximum iterations.

Do not symmetrize the transition matrix before clustering.

MCL switch to sparse matrix computation.

Some stats about the connected components in MCL.

Flag: --memory-intervals

Enable mid-sensitive mode.

Flag: --min-band-overlap

Flag: --minimizer-window

Minimum identity percentage to report an alignment.

Minimum query cover percentage to report an alignment.

Minimum subject cover percentage to report an alignment.

Flag: --min-len-ratio

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

Flag: --min-realign-overhang

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

Flag: --min_task_trace_pts

Key: --mmseqs-compat

Enable more sensitive mode.

TODO: this flag appears to be unused.

Softmask abundant motifs.

Initialize multiprocessing run.

Process only a single query chunk as specified

Enable continuation of interrupted multiprocessing run.

Flag: --mp-self

enable distributed-memory parallel processing

Flag: --narrow-band-cov

Flag: --narrow-band-factor

Flag: --neighborhood-score

TODO: this flag appears to be unused.

Flag: --no_8bit_extension

Disable auto appending of DAA and DMND file extensions.

Key: --no-block-size-limit

Flag: --no_chaining_merge_hsps

Flag: --no-dict

Flag: --no-forward-fp

Flag: --no-logfile

Print raw seqids without parsing

Disable ranking heuristic.

Flag: --no-reextend

Flag: --no-ref-masking

Flag: --no-reorder

Suppress reporting of identical self hits.

Flag: --no-swipe-realign

Do not unlink temporary files.

Flag: --oid-list

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.

Flag: --outfmt | -f

Flag: --output-fp

Flag: --output-hits

Flag: --palign

Directory for temporary files used by multiprocessing.

Flag: --path-cutoff

Flag: --p_best

BlastN mismatch penalty

Flag: --pipeline-short

Flag: --prefix-scan

Input query file.

Flag: --query-count

Genetic code to use to translate query.

Flag: --query-match-distance-threshold

Flag: --query-memory

Flag: --query-or-subject-cover

Flag: --query-parallel-limit

Disable all terminal output.

Flag: --radix-bits

Flag: --radix-cluster-buffered

Percentage of query range to be covered for range culling.

Restrict hit culling to overlapping query ranges.

Flag: --rank-factor

Flag: --ranking-cutoff-bitscore

Flag: --score-drop-factor

Flag: --raw

Flag: --reassign-max

Flag: --reassign-overlap

Flag: --reassign-ratio

Flag: --relaxed-evalue-factor

Filter out top FLOAT fraction of repetitive minimizers.

Report unaligned queries.

TODO: this flag appears to be unused.

Flag: --reverse

BlastN match reward

Flag: --rho

Flag: --roc-file

Add the query length to the SAM format (tag ZQ).

Flag: --score-estimate-factor

Flag: --score-ratio

Cutoff for seed complexity.

Flag: --seed-hit-density

Flag: --seed-weight | -w

Flag: --self

Enable sensitive mode.

Aligner sensitivity.

Filter the database by list of accessions.

Seed shapes

Number of seed shapes.

Enable mode using 30 seed shapes of weight 10

Flag: --short-query-max-len

Flag: --short-query-ungapped-bitscore

Flag: --short-seqids

Flag: --simple-freq

Flag: --sketch-size

Ignore accessions missing in the database.

Soft masking.

Flag: --sort-join

Flag: --space-penalty

Set the match score of stop codons against each other.

Flag: --store-query-quality