## Trim primers and barcodes and filter reads

### Description

Given a fasta, qual and oligos file, this tool trims primers and barcodes and filters reads for several criteria, including uniqueness.

### Parameters

- Use reverse complement (yes, no) [no]
- Minimum average quality of sequence (0-40) []
- Minimum average quality of window (Integer) []
- Window size (Integer) []
- Window step size (Integer) []
- Maximum ambiguous bases (0-10) []
- Maximum homopolymer length (0-50) []
- Minimum sequence length (0-1000) []
- Maximum sequence length (0-1000) []
- Maximum differences to primer sequences (0-10) []
- Maximum differences to barcode sequences (0-10) []

### Details

Trims primers and barcodes provided in an oligos-file, and filters out reads which don't fulfill the user-defined criteria. Also duplicate reads are removed and a count_table is produced showing how many times each representative sequence occurs in the different samples.

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

### Output

The analysis output consists of the following files:

- trim.unique.fasta: Trimmed and filtered unique sequences.
- trim.groups: List showing from which sample each sequence comes from.
- trim.unique.count_table: Table showing how many times each representative sequence occurs in the different samples.
- 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.