denoise.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.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/]

--method

Method to use for denoising. Choice of pyronoise or fast [default: fast]

-k, --keep_intermediates

Do not delete intermediate files – useful for debugging [default: False]

-c, --cut-off

Cut-off value (passed to pyroNoise) [default: 0.05]

-s, --precision

Precision (passed to pyroNoise)[default: 15.0]

-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] when method is fast

-p, --primer

Primer sequence [default: None]

Output:

This script results in a OTU 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:

denoise.py -i 454Reads.sff.txt

Multi-core Example:

Denoise flowgrams in file 454Reads.sff.txt using 2 cores on your machine in parallel (requires mpirun):

denoise.py -n 2 -i 454Reads.sff.txt