FStitch statistics

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Citations per year

Number of citations per year for the bioinformatics software tool FStitch

Tool usage distribution map

This map represents all the scientific publications referring to FStitch per scientific context
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FStitch specifications


Unique identifier OMICS_10575
Name FStitch
Alternative name Fast Read Stitcher
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data FStitch requires a BedGraph file.
Operating system Unix/Linux
Programming languages C++
Parallelization OpenMP
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Joseph Azofeifa

Publication for Fast Read Stitcher

FStitch citations


Genome wide dose dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super enhancers

Nucleic Acids Res
PMCID: 5829637
PMID: 29240919
DOI: 10.1093/nar/gkx1225

[…] The FStitch algorithm () was used to identify genomic regions enriched with H3K9ac and –K27ac signal from HCT116 ChIP-seq experiments. In order to acquire uniform FStitch signal calls across experiments t […]


A generative model for the behavior of RNA polymerase

PMCID: 5942361
PMID: 27663494
DOI: 10.1093/bioinformatics/btw599

[…] our model on publicly available biological data. To perform model inference of RNAP location requires an interval [a,b] where GRO-seq read mapping data (D) can be collected. To this end, we utilized Fast Read Stitcher (FStitch) that implements a maximum entropy Markov model to segment the genome into ‘transcribed regions’ (, ). In a HCT116 GRO-seq dataset (), FStitch classified 19 709 transcribed […]

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FStitch institution(s)
University of Colorado, Boulder, CO, USA

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