metashot/prok-annotate workflow

A Nextflow pipeline for the functional annotation of prokaryotic genomes and metagenomes.

Cite as:

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Main features

• Input: prokaryotic contig/genomes in FASTA format;
• Functional annotation using Prokka;
• Functional annotation through orthology assignment by eggNOG-mapper v2 and the eggNOG v5.0 database (optional);
• KEGG ortholog assignment by KofamScan and the KOfam database (https://www.genome.jp/tools/kofamkoala/) (optional);
• Estimates KEGG pathway completeness using Anvi'o (https://merenlab.org/software/anvio/) (optional);
• Automatic database download.

Quick start

Prokka only

1. Install Docker (or Singulariry) and Nextflow (see Dependences);

2. Start running the analysis (Prokka only, bacteria mode):

   nextflow run metashot/prok-annotate \
     --genomes "data/*.fa" \
     --outdir results

Documentation

Run eggNOG, KofamScan and Anvi'o Kofam

eggNOG, KofamScan and Anvi'o Kofam annotations can be performed by setting --run_eggnog, --run_kofamscan and --run_anvio_kofam options:

  nextflow run metashot/prok-annotate \
    --genomes "data/*.fa" \
    --run_eggnog \
    --run_kofamscan \
    --run_anvio_kofam \
    --outdir results

EggNOG, KofamScan and Anvi'o Kofam databases will be automatically downloaded from the Internet and and they will be put in the dbs directory in the results folder. If you want to download the databases manually, run the following lines:

• EggNOG:

  docker run --rm -v /path/to/eggnog_db:/eggnog_db metashot/eggnog-mapper:2.0.1-3 \
    python /eggnog_mapper/download_eggnog_data.py -y --data_dir /eggnog_db

  Add --eggnog_db /path/to/eggnog_db option to the nextflow run command.

• KofamScan

  Download KOfam database from ftp://ftp.genome.jp/pub/db/kofam/ and decompress it (e.g. into the /path/to/kofamscan_db folder:

  mkdir /path/to/kofamscan_db
  curl -s -L ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz | \
    tar -zxf - -C /path/to/kofamscan_db
  curl -s -L ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz -o ko_list.gz && \
    gunzip -c ko_list.gz > /path/to/kofamscan_db/ko_list

  Add --kofamscan_db /path/to/kofamscan_db option to the nextflow run command.

• Anvi'o Kofam

  docker run --rm -v /path/to/anvio_kofam_db:/anvio_kofam_db metashot/metashot/anvio:7-2 \
    anvi-setup-kegg-kofams --kegg-data-dir /anvio_kofam_db

  Add --anvio_kofam_db /path/to/anvio_kofam_db option to the nextflow run command.

Metagenomes

For metagenomes, we suggest to run the pipeline using the --metagenome option using EggNOG mapper only:

  nextflow run metashot/prok-annotate \
    --genomes "contigs/*.fa" \
    --metagenome \
    --skip_prokka \
    --run_eggnog \
    --eggnog_db_mem \
    --outdir results

Parameters

See the file nextflow.config for the complete list of parameters.

Output

The files and directories listed below will be created in the output directory after the pipeline has finished.

Main

• prokka: Prokka outputs (documentation);
• eggnog_*.tsv: count matrix for each transferred annotation;
• kofamscan_hits.tsv: count matrix for KofamScan hits;
• anvio_kofam_hits.tsv: count matrix for Anvio Kofam hits;
• anvio_modules.tsv: module completeness matrix.

Secondary

• eggnog (if --run_eggnog): eggNOG outputs (documentation);
• kofamscan (if --run_kofamscan): KofamScan output (detail format);
• anvio (if --run_anvio_kofam): anvi-estimate-metabolism (https://merenlab.org/software/anvio/help/main/programs/anvi-estimate-metabolism/) outputs for each input genome (kofam_hits and modules formats). Moreover gene calls in FASTA and text format are reported (anvi-get-sequences-for-gene-calls and anvi-export-gene-calls).

System requirements

Please refer to System requirements for the complete list of system requirements options.