News and Announcements » – Denoise a flowgram file


This script will denoise a flowgram file in .sff.txt format, which is the output of sffinfo.

Usage: [options]

Input Arguments:



-i, --input_file
Path to flowgram files (.sff.txt), comma separated
-f, --fasta_file
Path to fasta file from


-o, --output_dir
Path to output directory [default: denoised_seqs/]
-n, --num_cpus
Number of CPUs [default: 1]
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]
Select Titanium defaults for denoiser, otherwise use FLX defaults [default: False]


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 if the users wishes to have a defined similarity threshold.


Denoise flowgrams in file 454Reads.sff.txt, discard flowgrams not in seqs.fna, and extract primer from map.txt: -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: -n 2 -i 454Reads.sff.txt -f seqs.fna -m map.txt