BlastN

Flag: --add-self-aln

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

Use chaining with extension.

Flag: --aln-out

Flag: --anchored-swipe

Flag: --anchor-score

Flag: --anchor-window

Flag: --ants

Flag: --approx-backtrace

Band for dynamic programming computation

Flag: --band-bin

Flag: --bcutoff

Number of query bins for seed search.

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

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

Flag: --cut-bar

Flag: --cutoff-score-8bit

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

Chunk size for adaptive ranking.

Extension algorithm (wfa, ksw=default)

Flag: --ext-yield

Flag: --family-cap

Flag: --family-counts

Flag: --family-map

File: --family-map-query

Flag: --fast-tsv

Trace point fetch size.

Flag: --file1

Flag: --file2

File buffer size in bytes.

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

Flag: --gapped-filter-diag-score

E-value threshold for gapped filter (auto)

Flag: --gapped-filter-evalue1

Flag: --gapped-filter-window

Flag: --graph-algo

Flag: --hamming-ext

Flag: --hard-masked

Flag: --hash_join_swap

Flag: --heartbeat

Minimum number of identities for stage 1 hit.

Flag: --idl

Flag: --idn

Flag: --idr

Ignore warnings

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

Flag: --log-evalue-scale

Flag: --log-extend

Flag: --log-query

Flag: --log-subject

Flag: --mapany

Flag: --max-cells

Maximum seed frequency.

Flag: --max-indirection

Flag: --max-motif-len

Flag: --max-swipe-dp

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

Flag: --min-band-overlap

Flag: --minimizer-window

Flag: --min-len-ratio

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

Flag: --min-realign-overhang

Flag: --min_task_trace_pts

TODO: this flag appears to be unused.

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.

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

Flag: --no-swipe-realign

Do not unlink temporary files.

Flag: --oid-list

Flag: --output-fp

Flag: --output-hits

Flag: --palign

Flag: --path-cutoff

Flag: --p_best

BlastN mismatch penalty

Flag: --pipeline-short

Flag: --prefix-scan

Flag: --query-count

Flag: --query-match-distance-threshold

Flag: --query-memory

Flag: --query-or-subject-cover

Flag: --query-parallel-limit

Flag: --radix-bits

Flag: --radix-cluster-buffered

Percentage of query range to be covered for range culling.

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.

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

Seed shapes

Flag: --short-query-max-len

Flag: --short-query-ungapped-bitscore

Flag: --short-seqids

Flag: --simple-freq

Flag: --sketch-size

Flag: --sort-join

Flag: --space-penalty

Set the match score of stop codons against each other.

Flag: --store-query-quality

Flag: --strict-gvc

Flag: --superblock

Flag: --swipe-chunk-size

Flag: --swipe-task-size

Maximum tandem repeat period to consider (50)

Minimum repeat probability for masking.

Use tantan masking in ungapped mode

Flag: --target-bias

Number of target sequences to fetch for seed extension.

Flag: --target_hard_cap

Enable target-indexed mode.

Flag: --target-parallel-verbosity

Maximum number of targets to report per species.

Flag: --tile-size

Flag: --timeout

Diamond subcommand.

Flag: --trace-pt-fetch-size

Flag: --transcript-len-estimate

Flag: --tree

Flag: --tsv-read-size

TODO: seems to only be used by benchmark?

Flag: --unaligned-targets

Flag: --ungapped-evalue

Flag: --ungapped-evalue-short

Flag: --ungapped-window

Flag: --upgma-dist

Flag: --upgma-edge-limit

Flag: --upgma-input

Flag: --use-dataset-field

Flag: --sw

Flag: --weighted-gvc

xDrop for ungapped alignment.

Use gnl|BL_ORD_ID| style format in XML output.

zDrop for gapped dna alignment