Skip to content
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
42 lines (25 sloc) 1.31 KB


PuFFIN - A Parameter-free Method to Build Genome-wide Nucleosome Maps from Paired-end Sequencing Data


PuFFIN is a command line tool for accurate placing of the nucleosomes based on the pair-end reads. It was designed to place non-overlapping nucleosomes using extra length information present in pair-end data-sets.

The tool is written in python. There are no special requirements except for python2.7+.

The software is freely available for academic use. The software is still in development and may contain bugs and not 100% bulletproof.


Clone this repo

git clone



The input file for the tool should contain the reads only for considered chromosome (contig) and is in a BED format obtained by simply parsing the BAM/SAM file (see for example).

Given that input reads are in input.bam, that contain only reads for particular chromosome

./ input.bam > input.bed
python input.bed

The output will be printed in input.bed.nucs using next column format:

<Position of the nucleosome center> <width of the peak> <confidence score> <"Fuzziness"> <Level of the curve that was used to detect nucleosome >


MIT © Anton Polishko

You can’t perform that action at this time.