denoiser_preprocess.py – Run phase of denoiser algorithm: prefix clustering

Description:

The script denoiser_preprocess.py runs the first clustering phase which groups reads based on common prefixes.

Usage: 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