## Metagenomics / Remove chrimeric sequences with Mothur

### Description

Given a fasta-formatted alignment file, removes chimeric sequences.

### Parameters

None

### Details

Removes chimeric sequences from an alignment using the uchime method and the 16S rRNA Silva gold reference set. Chimeric sequences are artifacts which contain parts of several sequences.

This tool is based on the Chimera.uchime and Remove.seqs commands of the Mothur package.

### Output

The analysis output consists of the following:

- chimeras-removed.fasta: Alignment with chimeras removed
- chimeras-removed-summary.tsv: Summary statistics for the 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.