The growing amount of genomic data has prompted a need for less demanding and user friendly functional annotators. At the present, it’s hard to find a pipeline for the annotation of multiple functional data, such as both enzyme commission numbers (E.C.) and orthologous identifiers (KEGG and eggNOG), protein names, gene names, alternative names, and descriptions. Here, we provide a new solution which combines different algorithms (BLAST, DIAMOND, HMMER3) and databases (UniprotKB, KOfam, NCBIFAMs, TIGRFAMs, and PFAM), and also overcome data download challenges. Arche analysis pipeline can accommodate advanced tools in a unique order, creating several advantages regarding to other commonly used annotators.

Before you download Arche (13Gb), make sure GeneMarkS-2 (GMS2) is working properly on your computer. As GMS2 requires a licence (free), you must download it manually

  Download GeneMarkS-2 and key from http://exon.gatech.edu/GeneMark/license_download.cgi
  tar xvfz gms2_linux_[version].tar.gz

Move the dir to the desired place, and make the binary files accesible to your PATH (e.g. add export PATH=$PATH:</path/to/gms2_linux_[version]> to your ~/.bashrc file)

Configure the key you've downloaded

  gunzip gm_key.gz
  cp gm_key ~/.gmhmmp2_key
or   cp gm_key ~/.gm_key

Test the software

  gms2.pl --seq YOUR_GENOME

To install the other dependencies, you will require the anaconda distribution. Download and install it from https://www.anaconda.com/download/success

  conda create -n arche_annotator diamond=2.0.14 bedtools=2.27.0 p7zip=16.02 barrnap=0.9 hmmer=3.3.2 prodigal=2.6.3 blast=2.12.0 fasta3=36.3.8i ucsc-fasomerecords=455 trnascan-se=2.0.9 gdown -c bioconda -c conda-forge

This command wil create a conda environment for arche future runs. It includes the installation of specific packages from bioconda and conda-forge channels.

The program with the already formatted databases and mapping files can be downloaded (13Gb) via command line using gdown:

  conda activate arche_annotator
  gdown --fuzzy https://drive.google.com/file/d/1x9caXGPpYXCHUoodOdnuJI0tCDe9qtGG/view?usp=sharing

Once the download is finished:

  tar -xvf arche_[version].tar (move the output directory to the desired place)
  cd arche_[version]/bin/
  chmod +777 arche.sh
  ./arche.sh --install

You should make the bin directory accessible to your PATH (e.g. add export PATH=$PATH:</path/to/arche_[version]/bin> to your ~/.bashrc file)

In the case the instalation process or the running fails:

1. Check you are working within the conda environment you've created ("conda activate arche_annotator")
2. Check you have properly installed GeneMarkS-2
3. If you have already run the command ./arche.sh --install, open the arche.sh script using a text editor and in the section "Main directory" (first lines) replace the string after DIR= with the full path of the working directory, e.g. /home/YOUR_USER/arche_1.0.1
4. Delete arche's directory, uncompress from tar file, and install again

arche.sh -n ecoli -t 20 -r 40 e_coli.fna

arche.sh -n halorubrum -a ssearch -k achaea halorubrum_sp_DM2.fa

arche.sh -n seawater_meatgenome -k meta seawater_metagenome.fna

Here you can download a sample which includes the annotation of Escherichia coli K12 with several tools including Arche:

https://docs.google.com/spreadsheets/d/17Nd_y7w2axfxsjFJYAvb_NI3AW9HjNx4/edit?usp=sharing&ouid=115908476093915484477&rtpof=true&sd=true

The final table with all the annotations comes in two flavours:

[...]_omic_table.tbl which can be examined through the linux console with the comand

  column -ts "|" [example]_omic_table.tbl | less -S

[...]_omic_table.tsv which can be opened using spreadsheet editors like Microsoft Excel, LibreOffice Calc, etc.

-h, --help           This help.

-i, --install	     Set up the executable location, and install databases.

-n, --name-files     Name of the files to be created in the output directory, in-
		     cluding the directory itself (default 'arche').
             
-o, --output	     Provide the full path to the directory where the output di-
		     rectory will be created. E.g. /home/user/ (default current).
             
-k, --kingdom        Source of the contigs. Use 'arch' for archaeal genomes or
                         'meta' for metagenomes (default is for bacterial genomes).
                         
-m, --mode           Gives priority to Orthology (KO, eggNOG) or Enzyme Comission
                     designed databases during the annotation. Use 'kegg' for KO-->
                         eggNOG-->E.C., 'eggnog' for eggNOG-->KO-->E.C., or 'ec' for
                         E.C.-->KO-->eggNOG (default will use a shorter swiss-prot KO·
                         ·eggNOG·E.C. designed database with no priority).
                         
-a, --alignment      Select the algorithm to use during the protein alignment step:
                         'diamond' (accelerated blastp) or 'ssearch' (Smith-Waterman)
                         (default 'blastp').
                         
-t, --threads        Number of threads to use (default '1').

-r, --memory         Amount of RAM to use in GB (default '2').

-e, --evalue         Similarity e-value cut-off (default '1e-08').

-q, --query-cov      Minimum coverage on query protein (default '70').

-b, --bypass         Use 'yes' to bypass the RNA gene prediction.

-v, --verbose	     Use 'yes' to turn on the verbose mode.

GPL v3

• Daniel Alonso
• email: gundizalvus16@hotmail.com