denoise_wrapper.py – Denoise a flowgram file¶
Description:
This script will denoise a flowgram file in .sff.txt format, which is the output of sffinfo.
Usage: denoise_wrapper.py [options]
Input Arguments:
Note
[REQUIRED]
- -i, --input_file
- Path to flowgram files (.sff.txt), comma separated
- -f, --fasta_file
- Path to fasta file from split_libraries.py
[OPTIONAL]
- -o, --output_dir
- Path to output directory [default: denoised_seqs/]
- -n, --num_cpus
- Number of CPUs [default: 1]
- --force_overwrite
- Overwrite files in output directory [default: False]
- -m, --map_fname
- Name of mapping file, Has to contain field LinkerPrimerSequence. [REQUIRED unless –primer specified]
- -p, --primer
- Primer sequence [REQUIRED unless –map_fname specified]
- --titanium
- Select Titanium defaults for denoiser, otherwise use FLX defaults [default: False]
Output:
This script results in a OTU like mapping file along with a sequence file of denoised (FASTA-format). Note that the sequences coming from denoising are no real OTUs, and have to be sent to pick_otus.py if the users wishes to have a defined similarity threshold.
Example:
Denoise flowgrams in file 454Reads.sff.txt, discard flowgrams not in seqs.fna, and extract primer from map.txt:
denoise_wrapper.py -i 454Reads.sff.txt -f seqs.fna -m map.txt
Multi-core Example:
Denoise flowgrams in file 454Reads.sff.txt using 2 cores on your machine in parallel:
denoise_wrapper.py -n 2 -i 454Reads.sff.txt -f seqs.fna -m map.txt