multiPhate v1.1.0 Phage annotation

[mult1fractal]

what is multiPhATE

multiPhate

• fully automated computational pipeline for identifying and annotating phage genes in genome sequence
• controled by a configuration file, which can be tailored to run specific gene finders and to blast sequences against specific phage- and virus-centric data sets, in addition to more generic (genome, protein) data sets
• one gene finding algorithm, then annotates the genome, gene, and protein sequences using blast and a set of fasta sequence databases, and uses an hmm search against the pVOG database. If more than one gene finder is run, PhATE will also provide a side-by-side comparison of the genes called by each gene caller.
• Classification of each protein sequence into a pVOG group is followed by generation of an alignment-ready fasta file. By convention, genome sequence files end with extension, ".fasta"; gene nucleotide fasta files end with, ".fnt", and cds amino-acid fasta files end with, ".faa"

building in docker:

• build dockerfile with biopython, emboss, blast, glimmer, prodigal, hmmer, trnascan-se.
• using conda to setup everything except phanotate

needed databases:

• download autodatabases (blast hmm specify path to databases in file.config
  • NCBI virus genomes - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/
  • NCBI Refseq Protein - download using blast+: /bin/update_blastdb.pl refseq_protein
  • NCBI Refseq Gene - download using blast+: /bin/update_blastdb.pl refseqgene. This database contains primarily human sequences. To acquire bacterial gene sequences you may need to download them via http://ncbi.nlm.nih.gov/gene and process the data to generate a fasta data set. Support for doing this is not provided with the multiPhATE distribution
  • NCBI Swissprot - download using blast+: /bin/update_blastdb.pl swissprot
  • NR - ftp://ftp.ncbi.nlm.nih.gov/nr/
  • KEGG virus subset - (available by license) http://www.kegg.jp/kegg/download/
  • KEGG associated files - T40000.pep, T40000.nuc, vg_enzyme.list, vg_genome.list, vg_ko.list, vg_ncbi-geneid.list, vg_ncbi-proteinid.list, vg_pfam.list, vg_rs.list, vg_tax.list, vg_uniprot.list

[replikation]

• what about this: https://github.com/deprekate/PHANOTATE

[hoelzer]

triggered by PHANOTATE: here some notes from a recent virus meeting in the US, people are using/want to use currently

Identification of viral contigs

• VirSorter; Nontargeted Virus Discovery Pipeline; vFam
• VirFinder; DeepVirFinder; VIBRANT

Annotation of viruses

• VOGs (viral orthologous groups)
• Phannotate

Taxonomy

• Based on amino acid identity (vCONTACT)
• Based on phylogenetic trees of common viral genes (terminase, capsid, etc.)

[mult1fractal]

@replikation yup installtion via github