shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
MIT License
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Partition phage and eukaryotic viruses #57

Open shandley opened 2 years ago

shandley commented 2 years ago

In an early developmental version of hecatomb I merged the 'bigtable' (wasn't called that at the time!) to a list of phage taxonomies. This added a column called virus_type that allowed for simple partitioning go phage-to-nonphage viruses.

This should be easy to implement the same way we add Baltimore classifications.

I have the original phage list that I used for this (below). Ampullaviridae Atkinsviridae Autographiviridae Autolykiviridae Bicaudaviridae Blumeviridae Caudovirales Caudovirales_undefined_family Clavaviridae Corticoviridae Crevaviridae Cystoviridae Duinviridae Fiersviridae Fuselloviridae Globuloviridae Guelinviridae Guttaviridae Inoviridae Intestiviridae Jelitoviridae Leviviridae Ligamenvirales Ligamenvirales_undefined_family Lipothrixviridae Matshushitaviridae Microviridae Myoviridae Paulinoviridae Picobirnaviridae Plasmaviridae Pleolipoviridae Podoviridae Portogloboviridae Rountreeviridae Rudiviridae Salasmaviridae Schitoviridae Simuloviridae Siphoviridae Solspiviridae Sphaerolipoviridae Spiraviridae Steigviridae Steitzviridae Suoliviridae Tectiviridae Tinaiviridae Tristromaviridae Tubulavirales Tubulavirales_undefined_family Turriviridae unidentified phage Zobellviridae

beardymcjohnface commented 2 years ago

Do we need an expanded list for all the taxonkit outputs like "unclassified caudovirales family"?