SEA-PHAGES | Whole phage starterator reports

Link to this post \| posted yesterday, 22:38
cdshaffer	TL;DR: improvements to the back-end now allow for whole phage starterator reports to be generated for all new phage. See phage list at bottom to see if your phage is in release 583. Reports can be found at https://wustl.box.com/v/Actino-phage I have had some time to update the infrastructure and get Starterator to run inside a Docker container. This has allowed me to move the processing to the WashU cluster with significantly more processing power. I have added code to now run "Whole phage" reports in bulk on every new phage. As an initial release I am posting the whole phage reports for all phage which have been added since early Dec 2024. The whole phage reports, focus the starterator results on a single phage and have three benefits. First, the reports will sort the image section so that track #1 will be the gene for your phage. Thus, users will not have to sort through the tracks to find their gene. Secondly, the summary notes have been shortened to only your phage making this section shorter and easier to read. Finally there is a table generated near the start of the report which examines the current annotated start and compares it to the other manually annotated starts from that pham and summarizes that comparison. This allows for very rapid identification of starts that agree with the consensus found within the pham and those which do not. The downside is that for large phage from large clusters the whole phage report itself can be large and cumbersome so depending on your phage it may still work better for you and your students to use the individual pham reports. I have generated reports for all phage added since early December. See the complete list below. Here is the folder: https://wustl.box.com/v/Actino-phage P.S. If you have an older phage and would like a whole phage starterator report let me know by email and I will add it to the next run. Also all questions/comments/suggestions should be sent to me. Chris Shaffer Here is the list of phage found is this collection: Ablatia, Acai, AdaS, Akino08, Alatato, Amo99, AngelCake, Artiphact, Astralis, Axiom, BabyMoney, BaronJohn, Beleetus, Belieber, BetterYeti, BigDome, Bimmel, BlessJoy, BlueShadow, Bouchard, CallaLilly, CarisSwetlik, Carrillo, Caspiboi, ChickenTender, Chilliams, Chlochlo, ChocoMunchkin, Circuit, Citrus, CookieDog, CupcakePrincess, Dancer, Demure, Destructrice, DillyDally, DirtPie, Dodo, DogYard, EGUnicorn, ELee24, ElectricPheel, EmoNemo, ForDig, Forrestell, FosterFrank, FreakyGoo, FuegoCuervo, GUPitcher, Gandionco, Garnacho, Gavriela, Glorp, Glotell, GoldDust, GoldenEssence, Goodgraces, GoongGoong, Gravel, Greenbelt, Guzman, Gwennie1, Halloweekend, HamCheese, HazuAndZazu, HollowPurple, HotPotato, Ichiang, Invectra, Iridessa, IsHungry, Issa7, Jabb, Jakelyne, Jankie, Jesabah, JessellCookie, Jezreel, Jingles, KNG13, KSunshine22, KendraB23, KevinMinion, Khan1, Kinny, Koan, Kolhan, Kropertea, Kubulix, LadyAstra, LeoJr, Lethe, LilSmirk, Linayshia, Lishka, LordBart, Losacky, LucySwiss, Lukepolites, MacKat, MajinBuu, MakCheese, Marsus, Maruru, MaterMagnus, Mesmerelda, MiamiPanther, Moonflower, MsUbiquitous, Myram, Natasha, Nathan, Navi1117, NoSwimming, Nostromo, Nova53, November, Ollypop, Olympi, Pelletreau, Phanita, PhedwardCullen, PhigPhack, PhillyJawn, Phroglets, Pochacco, Poochiewood, Powelldog, PrairieDogTown, Raid, Rattail, RazorC, RazzB, RedRaider, RenegadeRaider, Rikishi, Riptide, Rita130, Rockabye, RustyBoy, SVoro, Scissor2024, Scotia, Scuba, Seldom, SenorClean, Shaffner, ShawBrad, Shrubaron, Shuckle, ShyRosie, SilentWarrior, SirFrank, Skitty, Smelly, Softsoap, Spooks, Starburst, StuartMinion, Sunshine23, SwainyDoc, SwissCheezer, Symere, Talon44, Talos, TicTac, TinaBug, TinyTerror, Toad24, Toneprano, Towmatter, TownLake, Trackstar, TriFive, Tubberson, Underpass, Utopia, Vitaenoii, Vitus, Vivum, WaddleDee, Wardwill, Westrich, Westy, Windest, Worcestershire, Wrackline, Yeshua, Zahlia, Zebo, Zhuangyuan, Zippen, Zodiariah, Edited yesterday, 22:40

Link to this post | posted yesterday, 22:38

TL;DR: improvements to the back-end now allow for whole phage starterator reports to be generated for all new phage. See phage list at bottom to see if your phage is in release 583. Reports can be found at https://wustl.box.com/v/Actino-phage

I have had some time to update the infrastructure and get Starterator to run inside a Docker container. This has allowed me to move the processing to the WashU cluster with significantly more processing power.

I have added code to now run "Whole phage" reports in bulk on every new phage. As an initial release I am posting the whole phage reports for all phage which have been added since early Dec 2024.

The whole phage reports, focus the starterator results on a single phage and have three benefits. First, the reports will sort the image section so that track #1 will be the gene for your phage. Thus, users will not have to sort through the tracks to find their gene. Secondly, the summary notes have been shortened to only your phage making this section shorter and easier to read. Finally there is a table generated near the start of the report which examines the current annotated start and compares it to the other manually annotated starts from that pham and summarizes that comparison. This allows for very rapid identification of starts that agree with the consensus found within the pham and those which do not.
The downside is that for large phage from large clusters the whole phage report itself can be large and cumbersome so depending on your phage it may still work better for you and your students to use the individual pham reports.

I have generated reports for all phage added since early December. See the complete list below.

Here is the folder:
https://wustl.box.com/v/Actino-phage
P.S. If you have an older phage and would like a whole phage starterator report let me know by email and I will add it to the next run. Also all questions/comments/suggestions should be sent to me.

Chris Shaffer

Here is the list of phage found is this collection:

Ablatia, Acai, AdaS, Akino08, Alatato, Amo99, AngelCake, Artiphact, Astralis,
Axiom, BabyMoney, BaronJohn, Beleetus, Belieber, BetterYeti, BigDome, Bimmel,
BlessJoy, BlueShadow, Bouchard, CallaLilly, CarisSwetlik, Carrillo, Caspiboi,
ChickenTender, Chilliams, Chlochlo, ChocoMunchkin, Circuit, Citrus, CookieDog,
CupcakePrincess, Dancer, Demure, Destructrice, DillyDally, DirtPie, Dodo,
DogYard, EGUnicorn, ELee24, ElectricPheel, EmoNemo, ForDig, Forrestell,
FosterFrank, FreakyGoo, FuegoCuervo, GUPitcher, Gandionco, Garnacho, Gavriela,
Glorp, Glotell, GoldDust, GoldenEssence, Goodgraces, GoongGoong, Gravel,
Greenbelt, Guzman, Gwennie1, Halloweekend, HamCheese, HazuAndZazu,
HollowPurple, HotPotato, Ichiang, Invectra, Iridessa, IsHungry, Issa7, Jabb,
Jakelyne, Jankie, Jesabah, JessellCookie, Jezreel, Jingles, KNG13, KSunshine22,
KendraB23, KevinMinion, Khan1, Kinny, Koan, Kolhan, Kropertea, Kubulix,
LadyAstra, LeoJr, Lethe, LilSmirk, Linayshia, Lishka, LordBart, Losacky,
LucySwiss, Lukepolites, MacKat, MajinBuu, MakCheese, Marsus, Maruru,
MaterMagnus, Mesmerelda, MiamiPanther, Moonflower, MsUbiquitous, Myram,
Natasha, Nathan, Navi1117, NoSwimming, Nostromo, Nova53, November, Ollypop,
Olympi, Pelletreau, Phanita, PhedwardCullen, PhigPhack, PhillyJawn, Phroglets,
Pochacco, Poochiewood, Powelldog, PrairieDogTown, Raid, Rattail, RazorC, RazzB,
RedRaider, RenegadeRaider, Rikishi, Riptide, Rita130, Rockabye, RustyBoy,
SVoro, Scissor2024, Scotia, Scuba, Seldom, SenorClean, Shaffner, ShawBrad,
Shrubaron, Shuckle, ShyRosie, SilentWarrior, SirFrank, Skitty, Smelly,
Softsoap, Spooks, Starburst, StuartMinion, Sunshine23, SwainyDoc, SwissCheezer,
Symere, Talon44, Talos, TicTac, TinaBug, TinyTerror, Toad24, Toneprano,
Towmatter, TownLake, Trackstar, TriFive, Tubberson, Underpass, Utopia,
Vitaenoii, Vitus, Vivum, WaddleDee, Wardwill, Westrich, Westy, Windest,
Worcestershire, Wrackline, Yeshua, Zahlia, Zebo, Zhuangyuan, Zippen, Zodiariah,

Edited yesterday, 22:40

Link to this post \| posted yesterday, 22:52
debbie	Thanks Chris! This is awesome! best, debbie

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Whole phage starterator reports