q2-assembly

bokulich-lab

CI codecov Code style: black

QIIME 2 plugin for (meta)genome assembly.

Installation

q2-assembly is available as part of the QIIME 2 moshpit distribution. For installation and usage instructions please consult the official QIIME 2 documentation.

Functionality

This QIIME 2 plugin contains actions used to assemble (meta)genomes from short single/paired-end sequencing reads:

ActionDescriptionUnderlying tool
assemble-megahitAssemble contigs using MEGAHIT.MEGAHIT
assemble-spadesAssemble contigs using SPAdes.SPAdes
evaluate-contigsEvaluate quality of the assembled contigs using metaQUAST.QUAST
generate-readsSimulate NGS reads using InSilicoSeq.InSilicoSeq
index-contigsIndex contigs using Bowtie 2.Bowtie 2
index-derep-magsIndex dereplicated MAGs using Bowtie2.Bowtie 2
index-magsIndex MAGs using Bowtie 2.Bowtie 2
map-readsMap reads to contigs/MAGs using Bowtie 2.Bowtie 2
rename-contigsRename contigs using unique IDs.-

Dev environment

This repository follows the black code style. To make the development slightly easier there are a couple of pre-commit hooks included here that will ensure that your changes follow that formatting style. Before you start working on the code, please install the hooks by executing make dev in your conda environment. From then on, they will be run automatically every time you commit any changes.

CI codecov Code style: black

QIIME 2 plugin for (meta)genome assembly.

Installation

q2-assembly is available as part of the QIIME 2 moshpit distribution. For installation and usage instructions please consult the official QIIME 2 documentation.

Functionality

This QIIME 2 plugin contains actions used to assemble (meta)genomes from short single/paired-end sequencing reads:

ActionDescriptionUnderlying tool
assemble-megahitAssemble contigs using MEGAHIT.MEGAHIT
assemble-spadesAssemble contigs using SPAdes.SPAdes
evaluate-contigsEvaluate quality of the assembled contigs using metaQUAST.QUAST
generate-readsSimulate NGS reads using InSilicoSeq.InSilicoSeq
index-contigsIndex contigs using Bowtie 2.Bowtie 2
index-derep-magsIndex dereplicated MAGs using Bowtie2.Bowtie 2
index-magsIndex MAGs using Bowtie 2.Bowtie 2
map-readsMap reads to contigs/MAGs using Bowtie 2.Bowtie 2
rename-contigsRename contigs using unique IDs.-

Dev environment

This repository follows the black code style. To make the development slightly easier there are a couple of pre-commit hooks included here that will ensure that your changes follow that formatting style. Before you start working on the code, please install the hooks by executing make dev in your conda environment. From then on, they will be run automatically every time you commit any changes.

CI codecov Code style: black

QIIME 2 plugin for (meta)genome assembly.

Installation

q2-assembly is available as part of the QIIME 2 moshpit distribution. For installation and usage instructions please consult the official QIIME 2 documentation.

Functionality

This QIIME 2 plugin contains actions used to assemble (meta)genomes from short single/paired-end sequencing reads:

ActionDescriptionUnderlying tool
assemble-megahitAssemble contigs using MEGAHIT.MEGAHIT
assemble-spadesAssemble contigs using SPAdes.SPAdes
evaluate-contigsEvaluate quality of the assembled contigs using metaQUAST.QUAST
generate-readsSimulate NGS reads using InSilicoSeq.InSilicoSeq
index-contigsIndex contigs using Bowtie 2.Bowtie 2
index-derep-magsIndex dereplicated MAGs using Bowtie2.Bowtie 2
index-magsIndex MAGs using Bowtie 2.Bowtie 2
map-readsMap reads to contigs/MAGs using Bowtie 2.Bowtie 2
rename-contigsRename contigs using unique IDs.-

Dev environment

This repository follows the black code style. To make the development slightly easier there are a couple of pre-commit hooks included here that will ensure that your changes follow that formatting style. Before you start working on the code, please install the hooks by executing make dev in your conda environment. From then on, they will be run automatically every time you commit any changes.

CI codecov Code style: black

QIIME 2 plugin for (meta)genome assembly.

Installation

q2-assembly is available as part of the QIIME 2 moshpit distribution. For installation and usage instructions please consult the official QIIME 2 documentation.

Functionality

This QIIME 2 plugin contains actions used to assemble (meta)genomes from short single/paired-end sequencing reads:

ActionDescriptionUnderlying tool
assemble-megahitAssemble contigs using MEGAHIT.MEGAHIT
assemble-spadesAssemble contigs using SPAdes.SPAdes
evaluate-contigsEvaluate quality of the assembled contigs using metaQUAST.QUAST
generate-readsSimulate NGS reads using InSilicoSeq.InSilicoSeq
index-contigsIndex contigs using Bowtie 2.Bowtie 2
index-derep-magsIndex dereplicated MAGs using Bowtie2.Bowtie 2
index-magsIndex MAGs using Bowtie 2.Bowtie 2
map-readsMap reads to contigs/MAGs using Bowtie 2.Bowtie 2
rename-contigsRename contigs using unique IDs.-

Dev environment

This repository follows the black code style. To make the development slightly easier there are a couple of pre-commit hooks included here that will ensure that your changes follow that formatting style. Before you start working on the code, please install the hooks by executing make dev in your conda environment. From then on, they will be run automatically every time you commit any changes.