- Command lines used to predict viruses from the HGAVD
- Same command lines were used for archaea Viruses downloaded from RefSeq database
- https://bitbucket.org/berkeleylab/checkv/src/master/
- Using a single command to run the full pipeline as recommended:
checkv end_to_end input_file.fna output_directory -t 16
conda activate CheckV
checkv end_to_end vir_1279.fna ../vir_1279_CheckV_Out -t 16
- https://github.com/jiarong/VirSorter2
- Quick Run : To run viral sequence identification on a test dataset
virsorter run -w test.out -i test.fa --min-length 1500 -j 4 all
conda activate vs2
virsorter run -w ../vir_1279_vs2_Out -i vir_1279.fna -j 4 all
- https://github.com/simroux/VirSorter
- To run VirSorter, type the following:
wrapper_phage_contigs_sorter_iPlant.pl -f assembly.fasta --db 1 --wdir output_directory --ncpu 4 --data-dir /path/to/virsorter-data
conda activate virsorter
wrapper_phage_contigs_sorter_iPlant.pl -f vir_1279.fna --db 1 --wdir ../vir_1279_vs_Out --ncpu 12 --data-dir ../virsorter-data
- https://github.com/AnantharamanLab/VIBRANT
- Test out a small dataset of mixed viral and non-viral scaffolds in nucleotide format
python3 VIBRANT_run.py -i example_data/mixed_example.fasta
conda activate VIBRANT
VIBRANT_run.py -i vir_1279.fna -folder ../vir_1279_VIBRANT_Out -t 16 -virome -d ../VIBRANT_db
- https://github.com/apcamargo/genomad
- The command to execute geNomad is structured like this:
genomad end-to-end [OPTIONS] INPUT OUTPUT DATABASE
conda activate genomad
genomad end-to-end --cleanup --splits 8 vir_1279.fna ../vir_1279_genomad_Out ../genomad_db/
conda activate ViralVerify
viralverify -f vir_1279.fna -o vir_1279_ViralVerify --hmm ../Pfam/nbc_hmms.hmm -p -t 10
-
archaea MAGs from the human gut detailed in:
-
https://www.ebi.ac.uk/metagenomics/genome-catalogues/human-gut-v2-0-1
-
To find repeats in short sequences, we need to decrease the minimum number of repeats to find. For example, in 100 bp reads, we could not possibly find more than 2 repeats:
-
minced -minNR 2 metagenome.fna -
the minced_parser script was used from https://github.com/Russel88/EsoPy
conda activate minced
for i in *.fa; do minced -minNR 2 $i ../Minced/"$i".crisprs ../Minced/"$i".gff; done
for i in *crisprs; do python minced_parser.py $i spacers > "$i".parsed.fa; done
conda activate BLAST
# make BLAST_DB out of vir_DB
makeblastdb -dbtype nucl -in vir_1279.fna -out vir_1279_DB
# BLAST spacers to vir_DB
for i in *.fa; do blastn -ungapped -out "$i"_blast_out -outfmt 7 -db vir_1279_DB -query $i; done
- https://github.com/eggnogdb/eggnog-mapper
- Run search and annotation for assembled contigs, using MMseqs2 "blastx" hits for gene prediction
emapper.py -m mmseqs --itype metagenome -i FASTA_FILE_NTS -o test
conda activate eggNOGmapper
emapper.py -i Hallmark_Genes_for_Archaeal_Virus.faa --itype proteins -o Hallmark_Genes_for_Archaeal_Virus_eggNOG.out -m mmseqs
- https://github.com/bbuchfink/diamond
- creating a diamond database our of the Viral Hallmark genes published by Li et al and using the database to scan the HGAVD.
conda activate eggNOGmapper
diamond makedb --in Hallmark_Genes_for_Archaeal_Virus.faa -d Hallmark_Genes_for_Archaeal_Virus_db
diamond blastx -d Hallmark_Genes_for_Archaeal_Virus_db.dmnd --fast -q vir_1279.fna -o DIAMOND_vir_1279_against_Hallmark_genes_matches_10e5_FINAL.csv -e 0.00001
- https://github.com/hyattpd/Prodigal
- Fast, reliable protein-coding gene prediction for prokaryotic genomes (-predict CDS of HGAVD viruses)
prodigal -i my.genome.fna -o my.genes -a my.proteins.faa
conda activate prokka
prodigal -i vir_1279.fna -o vir_1279.genes -a vir_1279.faa
- https://github.com/EddyRivasLab/hmmer
- Running hmmsearch against VOG HMMs
- downloaded from (https://vogdb.org/)
conda activate hmmer
for i in *.hmm; do hmmsearch --tblout "$i".hmm.out -E 1e-5 $i vir_1279.faa; done
- Running hmmsearch against VPF HMMs
- downloaded from (https://img.jgi.doe.gov//docs/final_list.hmms.gz)https://img.jgi.doe.gov//docs/final_list.hmms.gz
conda activate hmmer
hmmsearch --tblout vir_1279_against_VPF.hmm.out -E 1e-5 VPF_final_list.hmms vir_1279.faa; done
conda activate prokka
prodigal -i Zhang_X_2015_NM_ERR589874.NODE_1_560083.fna -o Zhang_X_2015_NM_ERR589874.NODE_1_560083.gbk -a Zhang_X_2015_NM_ERR589874.NODE_1_560083.faa
- Software used GenomeVx (http://wolfe.ucd.ie/GenomeVx/)
- Included information about hits to Li et al. Hallmark genes
- Included information about areas with matches to predicted CRISPR spacers from the human gut archaeome
- Included information about hits to VOGs confirmed by CheckV as well.
- -- Information is found in the output folder of the CheckV run under /tmp/gene_features.tsv.
- -- This output includes information on hits to the checkv-db (https://portal.nersc.gov/CheckV/)
- A detailed workbook for reproducing the figure is included in this repository (https://github.com/CynthiaChibani/HGUT_arch_viruses/blob/main/Zhang_X_2015_NM_ERR589874.NODE_1_560083_GenomeVX_details.xlsx)