-h, --help
Display the help message.
-hh, --full-help
Display the help message with advanced options.
--version
Display version information.
--copyright
Display long copyright information.
-v, --verbosityINTEGER
Display more/less diagnostic output during operation: 0 [only errors]; 1 [default]; 2 [+run-time,
options and statistics]. In range [0..2]. Default: 1.
InputOptions:-q, --queryINPUT_FILE
Query sequences. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*],
.ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the
following extensions: gz, bz2, and bgzf for transparent (de)compression.
-i, --indexINPUT_DIRECTORY
The database index (created by the 'lambda mkindexn' command). Valid filetype is: .lambda.
OutputOptions:-o, --outputOUTPUT_FILE
File to hold reports on hits (.m* are blastall -m* formats; .m8 is tab-separated, .m9 is tab-
separated with with comments, .m0 is pairwise format). Valid filetypes are: .sam[.*], .m9[.*],
.m8[.*], .m0[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for
transparent (de)compression. Default: output.m8.
--output-columnsSTRING
Print specified column combination and/or order (.m8 and .m9 outputs only); call -oc help for more
details. Default: std.
--percent-identityINTEGER
Output only matches above this threshold (checked before e-value check). In range [0..100].
Default: 0.
-e, --e-valueDOUBLE
Output only matches that score below this threshold. In range [0..100]. Default: 1e-04.
--bit-scoreDOUBLE
Output only matches that score above this threshold. In range [0..1000]. Default: 0.
-n, --num-matchesINTEGER
Print at most this number of matches per query. In range [1..10000]. Default: 256.
--sam-with-refheaderBOOL
BAM files require all subject names to be written to the header. For SAM this is not required, so
Lambda does not automatically do it to save space (especially for protein database this is a
lot!). If you still want them with SAM, e.g. for better BAM compatibility, use this option. One of
1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: off.
--sam-bam-seqSTRING
Write matching DNA subsequence into SAM/BAM file. If set to uniq than the sequence is omitted iff
it is identical to the previous match's subsequence. One of always, uniq, and never. Default:
uniq.
--sam-bam-tagsSTRING
Write the specified optional columns to the SAM/BAM file. Call --sam-bam-tags help for more
details. Default: ASNMaeaiqf.
--sam-bam-clipSTRING
Whether to hard-clip or soft-clip the regions beyond the local match. Soft-clipping retains the
full sequence in the output file, but obviously uses more space. One of hard and soft. Default:
hard.
GeneralOptions:-t, --threadsINTEGER
number of threads to run concurrently. Default: autodetected.
Seeding/Filtration:--adaptive-seedingBOOL
Grow the seed if it has too many hits (low complexity filter). One of 1, ON, TRUE, T, YES, 0, OFF,
FALSE, F, and NO. Default: off.
--seed-lengthINTEGER
Length of the seeds. In range [3..50]. Default: 14.
--seed-offsetINTEGER
Offset for seeding (if unset = seed-length/2). In range [1..50]. Default: 7.
--seed-deltaINTEGER
maximum seed distance. In range [0..1]. Default: 1.
--seed-delta-increases-lengthBOOL
Seed delta increases the min. seed length (for affected seeds). One of 1, ON, TRUE, T, YES, 0,
OFF, FALSE, F, and NO. Default: off.
--seed-half-exactBOOL
Allow errors only in second half of seed. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: on.
MiscellaneousHeuristics:--pre-scoringINTEGER
evaluate score of a region NUM times the size of the seed before extension (0 -> no pre-scoring, 1
-> evaluate seed, n-> area around seed, as well; default = 1 if no reduction is used). In range
[1..10]. Default: 2.
--pre-scoring-thresholdDOUBLE
minimum average score per position in pre-scoring region. In range [0..20]. Default: 2.
--filter-putative-duplicatesBOOL
filter hits that will likely duplicate a match already found. One of 1, ON, TRUE, T, YES, 0, OFF,
FALSE, F, and NO. Default: on.
--filter-putative-abundantBOOL
If the maximum number of matches per query are found already, stop searching if the remaining
realm looks unfeasible. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.
--merge-putative-siblingsBOOL
Merge seed from one region, stop searching if the remaining realm looks unfeasable. One of 1, ON,
TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.
Scoring:--score-gapINTEGER
Score per gap character. In range [-1000..1000]. Default: -2.
--score-gap-openINTEGER
Additional cost for opening gap. In range [-1000..1000]. Default: -5.
--score-matchINTEGER
Match score [only BLASTN]) In range [-1000..1000]. Default: 2.
--score-mismatchINTEGER
Mismatch score [only BLASTN] In range [-1000..1000]. Default: -3.
Extension:-x, --x-dropINTEGER
Stop Banded extension if score x below the maximum seen (-1 means no xdrop). In range [-1..1000].
Default: 30.
-b, --bandINTEGER
Size of the DP-band used in extension (-3 means log2 of query length; -2 means sqrt of query
length; -1 means full dp; n means band of size 2n+1) In range [-3..1000]. Default: -3.
-m, --extension-modeSTRING
Choice of extension algorithms. One of auto, xdrop, and fullSerial. Default: auto.
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