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.. _denoise_wrapper:
.. index:: denoise_wrapper.py
*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:** :file:`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 <./split_libraries.html>`_
**[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 <./pick_otus.html>`_ 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
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