Arche: a functional-optimized annotator for microbial meta(genomes)

Installing dependencies

Before you download Arche (13Gb), make sure the following software are working properly on your computer:

p7zip-full
bedtools >= 2.27.0
barrnap
Prodigal
hmmer
blastp
DIAMOND

FASTA36 ---> https://github.com/wrpearson/fasta36.git

faSomeRecords ---> The version which works with Arche can be found here http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

Infernal 1.1.4 ---> Install manually!
  tar xvfz infernal-1.1.4.tar.gz
  cd infernal-1.1.4/
  ./configure
  make
  sudo make install

tRNAscan-SE ---> Install manually!
  Download it from http://lowelab.ucsc.edu/tRNAscan-SE/
  tar xvfz trnascan-se-2.0.9.tar.gz
  cd tRNAscan-SE-2.0
  make
  sudo make install

GeneMarkS-2
  Download GeneMarkS-2 and key from http://exon.gatech.edu/GeneMark/license_download.cgi
  gunzip gm_key_64.gz
  tar xvfz gms2_linux_64.tar.gz
  cp gm_key_64 ~/.gmhmmp2_key

Installing Arche

The program with the already formatted databases and mapping files can be downloaded via GUI from Google Drive:

https://drive.google.com/file/d/1galIzwiuxXc3rNKyhoTysnl7DMdh3p4Z/view?usp=sharing

... or via command line using gdown:

  pip3 install gdown
  gdown --fuzzy https://drive.google.com/file/d/1x9caXGPpYXCHUoodOdnuJI0tCDe9qtGG/view?usp=sharing

Once the download is finished:

  tar -xvf arche_1.0.1.tar (move the output directory to the desired place)
  cd arche_1.0.1/bin/
  chmod +777 arche.sh
  ./arche.sh --install

You should make the script "arche.sh" accessible to your PATH, for example via symbolic link:

  cd /usr/bin
  sudo cp -s /home/???/???/arche_1.0.1/bin/arche.sh ./

ATTENTION! If something fails, you should check that all the dependencies are working, and repeat the installation process from the begining (arche_X.X.X.tar file).

Running Arche

BlastP annotation of a bacterial genome, using 20 threads and 40 GB of memory:

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

SSEARCH annotation of an archaeal genome, using 1 thread and 2 GB of memory

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

DIAMOND annotation of a metagenome

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

Annotation of Escherichia coli K12

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

Output Files

File(s)	Description
rRNA.tsv	GFF v3 file containing rRNA annotations.
rRNA.fna	FASTA file of all rRNA features.
tRNA.tsv	Table with tRNA details (coordinates, isotype, anticodon, scores, etc).
[...]_struc_annot.fna	FASTA file of all genomic features (nucleotide).
[...]_struc_annot.faa	FASTA file of translated coding genes (aminoacid).
heuristic[...]_out	Output matches of the search instance(s) performed with BLASTp, DIAMOND or SSEARCH36.
heuristic[...]_non_match.faa	FASTA file with the remaining non-matched sequences after the search instance(s) performed with BLASTp, DIAMOND or SSEARCH36.
hmmscan_[...]_out	HMMER3 output table of the search instance(s) performed against a specific HMMDB.
[HMMDB]_non_match.faa	FASTA file with the remaining non-matched sequences after the search instance performed against a specific HMMDB.
[...]_omic_table.tbl	Feature table with fields separated by vertical bars.
[...]_omic_table.tsv	Feature table with tab-separated fields.
arche_report	File which includes the parameters of the run and results.

Command line options

-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.

Licence

GPL v3

Author

• Daniel Alonso
• email: gundizalvus16@hotmail.com