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): Desvillechabrol et al, 2018: detection and characterization of genomic variations using running median and mixture models. GigaScience, 7(12), 2018. https://doi.org/10.1093/gigascience/giy110 For Sequanix: Desvillechabrol et al. 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) |
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Sequana includes a set of pipelines related to NGS (new generation sequencing) including quality control, variant calling, coverage, taxonomy, transcriptomics. We also ship Sequanix, a graphical user interface for Snakemake pipelines.
name/github | description | Latest Pypi version | Test passing | apptainers |
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sequana_pipetools | Create and Manage Sequana pipeline | Not required | ||
sequana-wrappers | Set of wrappers to build pipelines | Not on pypi | Not required | |
demultiplex | Demultiplex your raw data | License restriction | ||
denovo | denovo sequencing data | |||
fastqc | Get Sequencing Quality control | |||
LORA | Map sequences on target genome | |||
mapper | Map sequences on target genome | |||
nanomerge | Merge barcoded (or unbarcoded) nanopore fastq and reporting | |||
pacbio_qc | Pacbio quality control | |||
ribofinder | Find ribosomal content | |||
rnaseq | RNA-seq analysis | |||
variant_calling | Variant Calling | |||
multicov | Coverage (mapping) | |||
laa | Long read Amplicon Analysis | |||
revcomp | reverse complement of sequence data | |||
downsampling | downsample sequencing data | Not required | ||
depletion | remove/select reads mapping a reference |
name/github | description | Latest Pypi version | Test passing |
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trf | Find repeats | ||
multitax | Taxonomy analysis |
Please see the documentation for an up-to-date status and documentation.
Maintaining Sequana would not have been possible without users and contributors. Each contribution has been an encouragement to pursue this project. Thanks to all:
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0.17.3 |
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0.17.2 |
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0.17.1 |
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0.17.0 |
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0.16.9 |
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0.16.8 |
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0.16.7 |
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0.16.6 |
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0.16.5 |
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0.16.4 |
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0.16.3 |
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0.16.2 |
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0.16.1 |
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0.16.0 |
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0.15.4 |
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0.15.3 |
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0.15.2 |
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0.15.1 |
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0.15.0 |
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0.14.6 |
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0.14.5 |
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0.14.4 |
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0.14.3 |
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0.14.2 |
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0.14.1 |
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0.14.0 |
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0.13.X |
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0.12.X |
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