---
name: "lambda2-mkindexp"
section: "1"
platform: "linux"
package: "lambda-align2"
version: "2.0.1-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/lambda2-mkindexp"
---

# lambda2-mkindexp(1)

the Local Aligner for Massive Biological DatA

## NAME

lambda2\_mkindexp - the Local Aligner for Massive Biological DatA

## SYNOPSIS

**lambda2 mkindexp** \[*OPTIONS*\] -d DATABASE.fasta \[-i INDEX.lambda\]

## DESCRIPTION

*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\>*

*This is the indexer\_binary for creating lambda-compatible databases.*

## OPTIONS

- **-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:

- **-d***,* **--database** *INPUT\_FILE*

  *Database 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.*

- **-m***,* **--acc-tax-map** *INPUT\_FILE*

  *An NCBI or UniProt accession-to-taxid mapping file. Download from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ or ftp://ftp.uniprot.org/pub/databases/uniprot/current\_release/knowledgebase/idmapping/ . Valid filetypes are: .dat\[.\*\] and .accession2taxid\[.\*\], where \* is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.*

- **-x***,* **--tax-dump-dir** *INPUT\_DIRECTORY*

  *A directory that contains nodes.dmp and names.dmp; unzipped from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz*

### Output Options:

- **-i***,* **--index** *OUTPUT\_DIRECTORY*

  *The output directory for the index files (defaults to "DATABASE.lambda"). Valid filetype is: .lambda.*

- **--db-index-type** *STRING*

  *Suffix array or full-text minute space. One of fm and bifm. Default: fm.*

- **--truncate-ids** *BOOL*

  *Truncate IDs at first whitespace. This saves a lot of space and is irrelevant for all LAMBDA output formats other than BLAST Pairwise (.m0). One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.*

### Alphabets and Translation:

- **-a***,* **--input-alphabet** *STRING*

  *Alphabet of the database sequences (specify to override auto-detection); if input is Dna, it 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 generic). Default: 1.*

- **-r***,* **--alphabet-reduction** *STRING*

  *Alphabet Reduction for seeding phase. One of none and murphy10. Default: murphy10.*

### Algorithm:

- **--algorithm** *STRING*

  *Algorithm for SA construction (also used for FM; see Memory  Requirements below!). One of mergesort, quicksortbuckets, quicksort, radixsort, and skew7ext. Default: radixsort.*

- **-t***,* **--threads** *INTEGER*

  *number of threads to run concurrently. Default: autodetected.*

- **--tmp-dir** *OUTPUT\_DIRECTORY*

  *temporary directory used by skew, defaults to working directory.*

## REMARKS

*Please see the wiki (\<https://github.com/seqan/lambda/wiki\>) for more information on which indexes to chose and which algorithms to pick.*

*Note that the indexes created are binary and not compatible between different CPU endiannesses. Also the on-disk format is still subject to change between Lambda versions.*

## LEGAL

**lambda2 mkindexp 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**.