pyGeno: A Python package for precision medicine and proteogenomics [version 2; peer review: 1 approved, 2 approved with reservations]

pyGeno is a Python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-effi...

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Published inF1000 research Vol. 5; p. 381
Main Authors Daouda, Tariq, Perreault, Claude, Lemieux, Sébastien
Format Journal Article
LanguageEnglish
Published London Faculty of 1000 Ltd 2016
F1000Research
F1000 Research Ltd
Subjects
Bioinformatics
Genomics
Precision medicine
Protein Chemistry & Proteomics
Software Tool
python
database
proteomics
precision medicine
genomics
genetic polymorphisms
Bioinformatics
proteogenomics
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Summary:pyGeno is a Python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-efficient and fast framework, therefore allowing the user to easily explore subject-specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of Python, a general programming language. Its range of application therefore encompasses both short scripts and large scale genome-wide studies.
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TD designed and developed pyGeno. SL, CP, and TD contributed to the preparation of the manuscript. All authors were involved in the revision of the draft manuscript and have agreed to the final content.
Competing interests: No competing interests were disclosed.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.8251.2