Anvi'o Analysis Workflow Using Snakemake

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snakemake rules for running anvio

This Snakefile will run a basic anvi'o analysis of a set of assemblies and a set of samples, using the snakemake workflow manager.

Files

Snakefile

The file containing the snakemake rules

config.yaml.template

An example file containing the specific sample and assembly names that will be used in the workflow, as well as additional variable specifications.

Must be renamed 'config.yaml' for use.

cluster.json

A file specifying compute cluster job resource parameters for particular rules in the Snakefile.

requirements.txt

A file specifying conda requirements for the snakefile conda environment

launch.sh

Example launch command for launching on a Torque (qsub) job manager

anvio_install.sh

The commands I used for setting up my Anvi'o conda environment on Centos6

dag.svg

Visualization of the workflow steps run when executing the example config.yaml

data [directory]

Fake example data structure. For your own data, replace the files in data/assemblies and data/samples with the assembled contigs and the per-sample paired-end gzipped fastqs, respectively. Files must be named [assembly].fa and [sample].R[1,2].fq.gz

Code Snippets

shell:
    "tar -czf {output} {input}"

SnakeMake From line 29 of master/Snakefile

shell:
    "bowtie2-build {input} data/assemblies/{wildcards.assembly}"

SnakeMake Bowtie 2 From line 38 of master/Snakefile

shell:
    "bowtie2 -x {params.idx_base} -p {params.threads} --no-unal " \
              "-q -1 {input.R1} -2 {input.R2} | " \
              "samtools view -bS - > {output}"

SnakeMake SAMtools Bowtie 2 From line 53 of master/Snakefile

shell:
    "samtools sort -O bam -o {output} {input}"

SnakeMake SAMtools From line 63 of master/Snakefile

shell:
    "samtools index {input}"

SnakeMake SAMtools From line 71 of master/Snakefile

shell:
    "anvi-gen-contigs-database -f {input} -o {output}"

SnakeMake Anvio From line 79 of master/Snakefile

shell:
    """
    anvi-run-hmms -c {input} --num-threads {params.threads}
    """

SnakeMake Anvio From line 89 of master/Snakefile

shell:
    "anvi-get-dna-sequences-for-gene-calls -c {input} -o {output}"

SnakeMake Anvio From line 99 of master/Snakefile

shell:
    """
    export CENTRIFUGE_BASE={params.centrifuge_base}
    centrifuge -f --threads {params.threads} \
    -x {params.centrifuge_models} \
    {input.fa} \
    -S {output.hits} \
    --report-file {output.report}

    ln -s {output.hits} data/anvio/{wildcards.assembly}/centrifuge_hits.tsv
    ln -s {output.report} data/anvio/{wildcards.assembly}/centrifuge_report.tsv

    cd data/anvio/{wildcards.assembly}

    anvi-import-taxonomy -c {wildcards.assembly}.db \
    -i centrifuge_report.tsv centrifuge_hits.tsv \
    -p centrifuge

    rm centrifuge_hits.tsv
    rm centrifuge_report.tsv

    cd ../../../
    """

SnakeMake Anvio Centrifuge From line 114 of master/Snakefile

shell:
    """
    anvi-profile -i {input.sorted} \
    -c {input.db} \
    --overwrite-output-destinations \
    -o data/sorted_reads/{wildcards.assembly}.{wildcards.sample}.bam-ANVIO_PROFILE
    """

SnakeMake Anvio From line 148 of master/Snakefile

shell:
    """
    anvi-merge {input.profiles} \
    -o data/anvio/{wildcards.assembly}/SAMPLES_MERGED \
    -c {input.db} \
    -W
    """

SnakeMake Anvio From line 168 of master/Snakefile

shell:
    """
    anvi-summarize -p {input.prof} \
    -c {input.db} \
    -o data/anvio/{wildcards.assembly}/{wildcards.assembly}_SAMPLES-SUMMARY \
    -C CONCOCT
    """