Sequana documentation¶
Current version: 0.9.5, Dec 01, 2020
- Python version
Python 3.6, 3.7.3; most modules are Python2.7 compatible.
- Source
- Issues
Please fill a report on github
- How to cite
Citations are important for us to carry on developments. For Sequana library (including the pipelines), please use
Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352
For the genome coverage tool (sequana_coverage), please cite:
Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas Cokelaer Sequana coverage: detection and characterization of genomic variations using running median and mixture models GigaScience, Volume 7, Issue 12, December 2018, giy110, https://doi.org/10.1093/gigascience/giy110
For Sequanix (GUI for Snakemake pipeline), please cite:
Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer Sequanix: A Dynamic Graphical Interface for Snakemake Workflows Bioinformatics, bty034, https://doi.org/10.1093/bioinformatics/bty034 Also available on bioRxiv(DOI: https://doi.org/10.1101/162701)
Warning¶
- March 2020
Important notes for developers. Major refactoring for version 0.8 now pushed on master branch. Please use this new branch to create your own branches. If you still want to use the previous version, please checkout the branch master_20_03_2020 instead.
What is Sequana ?¶
Sequana is a versatile tool that provides
A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats).
A set of pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework) with more than 80 re-usable rules (see Rules).
Original tools to help in the creation of such pipelines including HTML reports.
- Standalone applications:
sequana_coverage ease the extraction of genomic regions of interest and genome coverage information
sequana_taxonomy performs a quick taxonomy of your FastQ. This requires dedicated databases to be downloaded.
Sequanix: GUI for snakemake workflows, a GUI for Snakemake workflows (hence Sequana pipelines as well)
The sequana pipelines are various. Since March 2020, they have their own independent life within dedicated github repositories. You may find pipelines for NGS quality control (e.g. adapters removal, phix removal, trimming of bad quality bases), variant calling, characterisation of the genome coverage, taxonomic classification, de-novo assembly, Variant calling, RNA-seq, etc. See the Pipelines section for more information.
Sequana can be used by developers to create new pipelines and by users in the form of applications ready for production. Moreover, Sequanix can be used to set the parameters of pipelines and execute them easily with a graphical user interface.
To join the project, please let us know on github.
Installation
conda install sequana
Examples
Visit our example gallery to use the Python library
NGS pipelines
Learn about available Snakemake pipelines
Standalone applications
Standalone applications including Sequanix (GUI for snakemake) and the sequana_coverage tool.
User guide and reference¶
- 1. Installation
- 2. Overview
- 3. Tutorial
- 4. Pipelines
- 5. Gallery
- 6. Case Examples
- 7. Applications (standalone)
- 8. Sequanix Tutorial
- 8.1. Quick Installation
- 8.2. Introduction
- 8.3. Sequana pipeline: the quality control example
- 8.4. Generic pipeline: a minimalist example with no configuration file
- 8.5. Generic pipeline: a minimalist example with a configuration file
- 8.6. Dialogs and running analysis locally or on a cluster
- 8.7. FAQS
- 9. Developer guide
- 10. Rules
- 11. References
- 11.1. Adapters
- 11.2. Assembly related
- 11.3. BAMTOOLS related
- 11.4. Coverage (bedtools module)
- 11.5. CIGAR tools
- 11.6. Coverage (theoretical)
- 11.7. Access to online database (e.g. ENA)
- 11.8. Enrichment
- 11.9. Experimental design
- 11.10. FASTQ module
- 11.11. FASTA module
- 11.12. Sequence module
- 11.13. Kmer module
- 11.14. IOTools module
- 11.15. Taxonomy related (Kraken - Krona)
- 11.16. Pacbio module
- 11.17. Phred quality
- 11.18. RNAdiff
- 11.19. Running median
- 11.20. Snakemake module
- 11.21. pipeline related module
- 11.22. Snpeff module
- 11.23. General tools
- 11.24. Format IO
- 11.25. VCF module
- 11.26. Module Reports
- 11.27. Wrapper to other tools
- 11.28. Misc
- 12. References (Viz)
- 13. References (stats)
- 14. FAQS
- 15. Changelog
- 16. Glossary