## Screen sequences for several criteria

### Description

Given a fasta file and a group/count file, this tool screens out sequences that do not fulfill user defined criteria.

### Parameters

- Minimum length
- Maximum length
- Alignment start position
- Alignment end position
- Optimize by (empty, minlength, start, end) [empty]
- Optimization criteria (0-100)
- Maximum number of ambiguous bases
- Maximum homopolymer length

### Details

Screen out sequences based on their length or alignment position. You can either choose the cut-off yourself (first four parameters), or use the optimization based on these. If you use the optimization, remember to determine the criteria: for example 85 means that Mothur will optimize the cutoff for the above chosen quality so that 85% of the sequences are kept.

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

### Output

The analysis output consists of the following:

- screened.fasta.gz: Compressed sequence file with the screened reads.
- screened.groups: If a group file was provided as input, a group file containing the names and sample assignment of sequences after screening will be provided.
- summary.screened.tsv: Summary statistics for the sequences.
- screened.count: If a count file was provided as input, a count file containing the names and numbers of unique sequences after screening will be provided.

### 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.