Provided by: lambda-align2_2.0.0-2build1_amd64
lambda2 searchp - the Local Aligner for Massive Biological DatA
lambda2 searchp [OPTIONS] -q QUERY.fasta -i INDEX.lambda [-o output.m8]
Lambda is a local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools. Detailed information is available in the wiki: <https://github.com/seqan/lambda/wiki>
-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, --verbosity INTEGER Display more/less diagnostic output during operation: 0 [only errors]; 1 [default]; 2 [+run-time, options and statistics]. In range [0..2]. Default: 1. Input Options: -q, --query INPUT_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. -a, --input-alphabet STRING Alphabet of the query sequences (specify to override auto-detection). Dna sequences will be translated. One of auto, dna5, and aminoacid. Default: auto. -g, --genetic-code INTEGER The translation table to use if input is Dna. See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for ids. Default is to use the same table that was used for the index or 1/CANONICAL if the index was not translated. Default: 0. -i, --index INPUT_DIRECTORY The database index (created by the 'lambda mkindexp' command). Valid filetype is: .lambda. Output Options: -o, --output OUTPUT_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. --output-columns STRING Print specified column combination and/or order (.m8 and .m9 outputs only); call -oc help for more details. Default: std. --percent-identity INTEGER Output only matches above this threshold (checked before e-value check). In range [0..100]. Default: 0. -e, --e-value DOUBLE Output only matches that score below this threshold. In range [0..100]. Default: 1e-04. -n, --num-matches INTEGER Print at most this number of matches per query. In range [1..10000]. Default: 256. --sam-with-refheader BOOL 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-seq STRING 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-tags STRING Write the specified optional columns to the SAM/BAM file. Call --sam-bam-tags help for more details. Default: AS NM ae ai qf. --sam-bam-clip STRING 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. General Options: -t, --threads INTEGER number of threads to run concurrently. In range [1..40]. Default: 4. Seeding / Filtration: --adaptive-seeding BOOL 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: on. --seed-length INTEGER Length of the seeds. In range [3..50]. Default: 10. --seed-offset INTEGER Offset for seeding (if unset = seed-length/2). In range [1..50]. Default: 5. --seed-delta INTEGER maximum seed distance. In range [0..1]. Default: 1. --seed-delta-increases-length BOOL 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-exact BOOL Allow errors only in second half of seed. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on. Miscellaneous Heuristics: --pre-scoring INTEGER 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-threshold DOUBLE minimum average score per position in pre-scoring region. In range [0..20]. Default: 2. --filter-putative-duplicates BOOL 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-abundant BOOL 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-siblings BOOL 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: -s, --scoring-scheme INTEGER use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80. Default: 62. --score-gap INTEGER Score per gap character. In range [-1000..1000]. Default: -1. --score-gap-open INTEGER Additional cost for opening gap. In range [-1000..1000]. Default: -11. Extension: -x, --x-drop INTEGER Stop Banded extension if score x below the maximum seen (-1 means no xdrop). In range [-1..1000]. Default: 30. -b, --band INTEGER 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-mode STRING Choice of extension algorithms. One of auto, xdrop, and fullSerial. Default: auto.
Tuning the seeding parameters and (de)activating alphabet reduction has a strong influence on both speed and sensitivity. We recommend the following alternative profiles for protein searches: fast (high similarity): --seed-delta-increases-length on sensitive (lower similarity): --seed-offset 3 For further information see the wiki: <https://github.com/seqan/lambda/wiki>
lambda2 searchp Copyright: 2013-2019 Hannes Hauswedell, released under the GNU AGPL v3 (or later); 2016-2019 Knut Reinert and Freie Universität Berlin, released under the 3-clause- BSDL SeqAn Copyright: 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL. In your academic works please cite: Hauswedell et al (2014); doi: 10.1093/bioinformatics/btu439 For full copyright and/or warranty information see --copyright.