QIIME 2 plugin for (meta)genome assembly.
Before q2-assembly is available from conda, follow the installation steps described below.
curl -sLH 'Accept: application/vnd.github.v3.raw' https://api.github.com/repos/bokulich-lab/q2-assembly/contents/requirements.txt > requirements.txtmamba create -yn q2-shotgun \
-c https://packages.qiime2.org/qiime2/2022.4/tested \
-c bioconda -c conda-forge -c default \
--file requirements.txt
conda activate q2-shotgunAdditionally, a patched version of quast is required, plus q2-types-genomics and q2-assembly itself:
pip install \
git+https://github.com/ablab/quast.git@de7e1f4891a3487f3c0df6ae27cbfba38734d686 \
git+https://github.com/bokulich-lab/q2-assembly.gitRefresh cache and check that everything worked:
qiime dev refresh-cache
qiime info