Bioconda: sustainable and comprehensive software distribution for the life sciences

By Ryan K. Dale, Björn A. Grüning, A. Sjödin, Jillian Rowe, Brad A. Chapman, C. Tomkins-Tinch, Renan Valieris, Bérénice Batut, A. Caprez, T. Cokelaer and 142 more. Nature Methods, 2018

1,435 citations recorded by the source corpus.

We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.

Subfields: Information Systems, Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d54ff996c472f4f48ab14418e3523037e2af880b

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In Information Systems

1. Anton Nekrutenko
2. Shujun Ou
3. Ning Jiang
4. Heng Li

In Information Systems and Management

1. Anton Nekrutenko

In Molecular Biology

1. Sergei L. Kosakovsky Pond
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Citations in the corpus

• The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024, neutral): “…Galaxy tool wrappers (via Planemo), Galaxy instance APIs (adding tool availability), ELIXIR bio.tools ( https:// bio.tools/ ) (adding EMBRACE Data And Methods’ (EDAM terms ( 3 )), BioConda ( 14 ) (checking if tools are current), and a community-curated worksheet (flag-ging tools to be excluded).”
• Twelve years of SAMtools and BCFtools (2020, methodology): “Both packages have been installed over a million times via Bioconda.”
• Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline (2019, methodology): “We found compile-free and precompiled programs were the 403 easiest to use, followed by those available via conda and bioconda [60].”
• Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization (2020, background): “Moreover, a command line version is provided by conda and is available via the bioconda channel (16).”
• BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes (2021, background): “Bioconda (Grüning et al. 2018) and Docker (Merkel 2014).”