## Align sequences

### Description

Given a fasta file of 16S rRNA sequences, aligns them to the Silva 16S rRNA reference alignment template. When using the Silva reference you should be aware of their dual-use license: Silva is free for academic users, but commercial users need to purchase a license.

### Parameters

- Reference (bacterial, full, own) [bacterial]
- Start position of your region of interest
- End position of your region of interest

### 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. You can use either the full reference or just the bacterial subsection of it. You can also provide your own reference alignment fasta. Please indicate the region of the reference alignment that your amplified region corresponds to, as this will improve the overall alignment quality and save space.

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.

The speed of this tool depends on the number and length of your sequences, and the number and length of the sequences in the reference template.

This tool is based on the Align.seqs and Pcr.seqs commands 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
- custom.reference.summary.tsv: Summary statistics for the reference alignment

### 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.