## Metagenomics / Trim and filter reads with Mothur

### Description

Trim and filter reads and remove duplicate reads.

### Parameters

- flip (yes, no) [no]
- qaverage (0-40) []
- qwindowaverage (Integer) []
- qwindowsize (Integer) []
- qstepsize (Integer) []
- maxambig (0-10) []
- maxhomop (0-50) []
- minlength (0-1000) []
- maxlength (0-1000) []
- pdiffs (0-10) []
- bdiffs (0-10) []

### Details

The reads are checked against user-defined requirements. The output sequences will be trimmed to remove the user-provided primers, barcodes, and sequences that do not meet the give ncriteria. The reads are also checked for redundancy. If a quality file is provided, a trimmed, non-redundant quality file is produce to match the trimmed, non-redundant sequence file.

This tool is based on the Trim.seqs and Unique.seqs commands of the Mothur package.

### Output

The analysis output consists of the following:

- reads.groups: A two column list with the first column indicating the sequence names in the input file and the second column the group that it came from.
- reads.trim.names: A list of the selected sequences and the redundant sequences corresponding to each.
- reads.trim.unique.fasta: A FASTA-formatted sequence file trimmed, non-redundant reads.
- reads.trim.unique.qual: Quality values (if provided as input) for the trimmed, non-redundant reads
- summary.trim.unique.tsv: Summary statistics for the 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.