-h, --help
Display the help message.
-hh, --full-help
Display the help message with advanced options.
--version-checkBOOL
Turn this option off to disable version update notifications of the application. One of 1, ON,
TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.
--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.
-d, --databaseINPUT_FILE
Path to original database sequences (a precomputed index with .sa or .fm needs to exist!). 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.
-di, --db-index-typeSTRING
database index is in this format. One of sa and fm. Default: fm.
OutputOptions:-o, --outputOUTPUT_FILE
File to hold reports on hits (.m* are blastall -m* formats; .m8 is tab-seperated, .m9 is tab-
seperated 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.
-oc, --output-columnsSTRING
Print specified column combination and/or order (.m8 and .m9 outputs only); call -oc help for more
details. Default: std.
-id, --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..inf]. Default: 0.1.
-nm, --num-matchesINTEGER
Print at most this number of matches per query. In range [1..inf]. Default: 500.
--sam-with-refheaderSTRING
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
on and off. Default: off.
--sam-bam-seqSTRING
Write matching DNA subsequence into SAM/BAM file (BLASTN). For BLASTX and TBLASTX the matching
protein sequence is "untranslated" and positions retransformed to the original sequence. For
BLASTP and TBLASTN there is no DNA sequence so a "*" is written to the SEQ column. The matching
protein sequence can be written as an optional tag, see --sam-bam-tags. 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: ASNMZEZIZF.
--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.
-qi, --query-index-typeSTRING
controls double-indexing. One of radix and none. Default: none.
AlphabetsandTranslation:-p, --programSTRING
Blast Operation Mode. One of blastn, blastp, blastx, tblastn, and tblastx. Default: blastx.
-g, --genetic-codeINTEGER
The translation table to use for nucl -> amino acid translation(not for BlastN, BlastP). See
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for ids (default is generic). Six
frames are generated. Default: 1.
-ar, --alphabet-reductionSTRING
Alphabet Reduction for seeding phase (ignored for BLASTN). One of none and murphy10. Default:
murphy10.
Seeding/Filtration:-sl, --seed-lengthINTEGER
Length of the seeds (default = 14 for BLASTN). Default: 10.
-so, --seed-offsetINTEGER
Offset for seeding (if unset = seed-length, non-overlapping; default = 5 for BLASTN). Default: 10.
-sd, --seed-deltaINTEGER
maximum seed distance. Default: 1.
MiscellaneousHeuristics:-ps, --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..inf]. Default: 2.
-pt, --pre-scoring-thresholdDOUBLE
minimum average score per position in pre-scoring region. Default: 2.
-pd, --filter-putative-duplicatesSTRING
filter hits that will likely duplicate a match already found. One of on and off. Default: on.
-pa, --filter-putative-abundantSTRING
If the maximum number of matches per query are found already, stop searching if the remaining
realm looks unfeasable. One of on and off. Default: on.
Scoring:-sc, --scoring-schemeINTEGER
use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; [ignored for BlastN]
Default: 62.
-ge, --score-gapINTEGER
Score per gap character (default = -2 for BLASTN). Default: -1.
-go, --score-gap-openINTEGER
Additional cost for opening gap (default = -5 for BLASTN). Default: -11.
-ma, --score-matchINTEGER
Match score [only BLASTN]) Default: 2.
-mi, --score-mismatchINTEGER
Mismatch score [only BLASTN] Default: -3.
Extension:-x, --x-dropINTEGER
Stop Banded extension if score x below the maximum seen (-1 means no xdrop). In range [-1..inf].
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..inf]. Default: -3.
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