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command lines tool to annotate miRNAs with a standard mirna/isomir naming
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data implement method to wirte gff line Jul 2, 2019
docs update to 1.2 mirgff3 version Jul 12, 2019
mirtop fix bug in trimming since 0.4.19 Jul 30, 2019
scripts fix bug in trimming since 0.4.19 Jul 30, 2019
test add test to check whether calling changes between versions Jul 30, 2019
.gitignore gix test unit Feb 15, 2019
.travis.yml cast map into list to avoid py3 errors Mar 13, 2019
LICENSE migrate miRNA annotation from seqcluster to mirtop Jun 24, 2016 update to 1.2 mirgff3 version Jul 12, 2019
requirements.txt Python 3 support: use six for encoding and basestring Jan 13, 2019 Fixes for testing Dec 9, 2016


Project Status: Active – The project has reached a stable, usable state and is being actively developed. biorxiv

Command line tool to annotate with a standard naming miRNAs e isomiRs.

This tool adapt the miRNA GFF3 format agreed on here:


Ask question, ideas Contributors to code



Everybody is welcome to contribute, fork the devel branch and start working!

If you are interesting in miRNA or small RNA analysis, you can jump into the incubator issue pages to propose/ask or say hi:


Join the team:

Read more:



conda install mirtop -c bioconda


pip install mirtop

develop version

Thes best solution is to install conda to get an independent enviroment.


bash -b -p ~/mirtop_env

export PATH=$PATH:~/mirtop_env

conda install -c bioconda pysam pybedtools pandas biopython samtools

git clone

cd mirtop

python develop

Quick start

Read complete commands at:

git clone mirtop
cd mirtop/data
mirtop gff --sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out sim_isomir.bam


The mirtop gff generates the GFF3 adapted format to capture miRNA variations. The output is explained here.



Here we cite any person who has contribute somehow to the project different than through code development and/or bioinformatic concepts.

Gianvito Urgese, Jan Oppelt(CEITEC Masaryk University, Brno, Czech Republic), Thomas Desvignes, Bastian, Kieran O'Neill (BC Cancer), Charles Reid (University of California Davis), Radhika Khetani (Harvard Chan School of Public Health), Shannan Ho Sui (Harvard Chan School of Public Health), Simonas Juzenas(CAU), Rafael Alis (Catholic University of Valencia), Aida Arcas (Instituto de Neurociencias (CSIC-UMH)), Yufei Lin (Harvard University), Victor Barrera(Harvard Chan School of Public Health), Marc Halushka (Johns Hopkins University)

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