---
name: "stellar"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/stellar"
---

# stellar(1)

the SwifT Exact LocaL AligneR

## NAME

stellar - the SwifT Exact LocaL AligneR

## SYNOPSIS

**stellar** \[*OPTIONS*\] \<*FASTA FILE 1*\> \<*FASTA FILE 2*\>

## DESCRIPTION

STELLAR implements the SWIFT filter algorithm (Rasmussen et al., 2006) and a verification step for the SWIFT hits that applies local alignment, gapped X-drop extension, and extraction of the longest epsilon-match.

Input to STELLAR are two files, each containing one or more sequences in FASTA format. Each sequence from file 1 will be compared to each sequence in file 2. The sequences from file 1 are used as database, the sequences from file 2 as queries.

(c) 2010-2012 by Birte Kehr

## REQUIRED ARGUMENTS

- **FASTA\_FILE\_1** *INPUT\_FILE*

   Valid filetypes are: *.fasta* and *.fa*.

- **FASTA\_FILE\_2** *INPUT\_FILE*

   Valid filetypes are: *.fasta* and *.fa*.

## OPTIONS

- **-h**, **--help**

  Display the help message.

- **--version**

  Display version information.

### Main Options:

- **-e**, **--epsilon** *DOUBLE*

  Maximal error rate (max 0.25). In range \[0.0000001..0.25\]. Default: *0.05*.

- **-l**, **--minLength** *INTEGER*

  Minimal length of epsilon-matches. In range \[0..inf\]. Default: *100*.

- **-f**, **--forward**

  Search only in forward strand of database.

- **-r**, **--reverse**

  Search only in reverse complement of database.

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

  Alphabet type of input sequences (dna, rna, dna5, rna5, protein, char). One of *dna*, *dna5*, *rna*, *rna5*, *protein*, and *char*.

- **-v**, **--verbose**

  Set verbosity mode.

### Filtering Options:

- **-k**, **--kmer** *INTEGER*

  Length of the q-grams (max 32). In range \[1..32\].

- **-rp**, **--repeatPeriod** *INTEGER*

  Maximal period of low complexity repeats to be filtered. Default: *1*.

- **-rl**, **--repeatLength** *INTEGER*

  Minimal length of low complexity repeats to be filtered. Default: *1000*.

- **-c**, **--abundanceCut** *DOUBLE*

  k-mer overabundance cut ratio. In range \[0..1\]. Default: *1*.

### Verification Options:

- **-x**, **--xDrop** *DOUBLE*

  Maximal x-drop for extension. Default: *5*.

- **-vs**, **--verification** *STRING*

  Verification strategy: exact or bestLocal or bandedGlobal One of *exact*, *bestLocal*, and *bandedGlobal*. Default: *exact*.

- **-dt**, **--disableThresh** *INTEGER*

  Maximal number of verified matches before disabling verification for one query sequence (default infinity). In range \[0..inf\].

- **-n**, **--numMatches** *INTEGER*

  Maximal number of kept matches per query and database. If STELLAR finds more matches, only the longest ones are kept. Default: *50*.

- **-s**, **--sortThresh** *INTEGER*

  Number of matches triggering removal of duplicates. Choose a smaller value for saving space. Default: *500*.

### Output Options:

- **-o**, **--out** *OUTPUT\_FILE*

  Name of output file. Valid filetypes are: *.txt* and *.gff*. Default: *stellar.gff*.

- **-od**, **--outDisabled** *OUTPUT\_FILE*

  Name of output file for disabled query sequences. Valid filetypes are: *.sam\[.\*\]*, *.raw\[.\*\]*, *.frn\[.\*\]*, *.fq\[.\*\]*, *.fna\[.\*\]*, *.ffn\[.\*\]*, *.fastq\[.\*\]*, *.fasta\[.\*\]*, *.faa\[.\*\]*, *.fa\[.\*\]*, and *.bam*, where \* is any of the following extensions: *gz*, *bz2*, and *bgzf* for transparent (de)compression. Default: *stellar.disabled.fasta*.

## REFERENCES

Kehr, B., Weese, D., Reinert, K.: STELLAR: fast and exact local alignments. BMC Bioinformatics, 12(Suppl 9):S15, 2011.