## Metagenomics / Align sequences with Mothur

### Description

Given a fasta file of 16S rRNA sequences, aligns them to the Silva 16S rRNA template sequence set.

### Parameters

None

### Details

Sequences in are aligned, one by one, against the Silva 16S rRNA reference set. Kmer searching with 8mers is followed by Needleman-Wunsch pairwise alignment, which penalizes the same amount for opening and extending a gap.

The alignment result is given in fasta format, with periods ('.') leading up to the first base in the sequence and following the last base of the sequence.

This tool is based on the Align.seqs command of the Mothur package.

### Output

The analysis output consists of the following:

- aligned.fasta: Aligned sequences
- aligned-summary.tsv: Summary statistics for the aligned sequences

### References

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.