- recipe sga
SGA - String Graph Assembler. SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers string graph formulation of assembly and uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads.
- package sga¶
- depends bamtools:
- depends libgcc-ng:
- depends libstdcxx-ng:
- depends libzlib:
- depends sparsehash:
- depends zlib:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install sga and update with:: mamba update sga
To create a new environment, run:
mamba create --name myenvname sga
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/sga:<tag> (see `sga/tags`_ for valid values for ``<tag>``)