recipe sina

Reference based multiple sequence alignment

Homepage:

https://github.com/epruesse/SINA

Documentation:

https://sina.readthedocs.io

License:

GPL / GPLv3

Recipe:

/sina/meta.yaml

Links:

biotools: SINA, doi: 10.1093/bioinformatics/bts252

SINA allows incorporating additional sequences into an existing multiple sequence alignment (MSA) without modifying the original alignment. While adding sequences to an MSA with SINA is usually faster than re-computing the entire MSA from an augmented set of unaligned sequences, the primary benefit lies in protecting investments made into the original MSA such as manual curation of the alignment, compute intensive phylogenetic tree reconstruction and taxonomic annotation of the resulting phylogeny.

Additionally, SINA includes a homology search which uses the previously computed alignment to determine the most similar sequences. Based on the search results, a LCA based classification of the query sequence can be computed using taxonomic classifications assigned to the sequences comprising the reference MSA.

SINA is used to compute the small and large subunit ribosomal RNA alignments provided by the SILVA_ project and is able to use the ARB_ format reference databases released by the project.

package sina

(downloads) docker_sina

Versions:
1.7.2-0,  1.7.1-0,  1.7.0-0,  1.6.1-0,  1.6.0-0,  1.5.0-0,  1.4.0-0,  1.3.5-2,  1.3.4-2, 

1.7.2-0,  1.7.1-0,  1.7.0-0,  1.6.1-0,  1.6.0-0,  1.5.0-0,  1.4.0-0,  1.3.5-2,  1.3.4-2,  1.3.1-2,  1.3.1-0,  1.3.0-0

Depends:

  • on arb-bio-tools

  • on boost-cpp >=1.70.0,<1.70.1.0a0

  • on glib >=2.58.3,<3.0a0

  • on libarbdb 6.0.6 haa8b8d8_8

  • on libgcc-ng >=7.5.0

  • on libstdcxx-ng >=7.5.0

  • on tbb >=2020.2,<2021.0.0a0

  • on zlib >=1.2.11,<1.3.0a0

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install sina

to add into an existing workspace instead, run:

pixi add sina

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install sina

Alternatively, to install into a new environment, run:

conda create -n envname sina

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/sina:<tag>

(see sina/tags for valid values for <tag>).

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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