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.. _denoiser_preprocess:
.. index:: denoiser_preprocess.py
*denoiser_preprocess.py* -- Run phase of denoiser algorithm: prefix clustering
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
The script `denoiser_preprocess.py <./denoiser_preprocess.html>`_ runs the first clustering phase
which groups reads based on common prefixes.
**Usage:** :file:`denoiser_preprocess.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_files
Path to flowgram files (.sff.txt), comma separated
**[OPTIONAL]**
-f, `-`-fasta_file
Path to fasta input file [default: None]
-s, `-`-squeeze
Use run-length encoding for prefix filtering [default: False]
-l, `-`-log_file
Path to log file [default: preprocess.log]
-p, `-`-primer
Primer sequence used for the amplification [default: CATGCTGCCTCCCGTAGGAGT]
-o, `-`-output_dir
Path to output directory [default: /tmp/]
**Output:**
prefix_dereplicated.sff.txt: human readable sff file containing the flowgram of the
cluster representative of each cluster.
prefix_dereplicated.fasta: Fasta file containing the cluster representative of each cluster.
prefix_mapping.txt: This file contains the actual clusters. The cluster centroid is given first,
the cluster members follw after the ':'.
Run program on flowgrams in 454Reads.sff. Remove reads which are not in split_lib_filtered_seqs.fasta.
Remove primer CATGCTGCCTCCCGTAGGAGT from reads before running phase I
::
denoiser_preprocess.py -i Fasting_Example.sff.txt -f seqs.fna -p CATGCTGCCTCCCGTAGGAGT
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