Pokémon manga (Japanese: マンガ manga), unlike the Pokémon anime, does not actually refer to one specific manga or one particular piece of Pokémon canon but, rather, an entire subcategory of comics written with their own storylines and interpretations of the Pokémon world. These frequently have no connection to one another beyond their medium.
From reading some of the manga, it feels that it's got more to do with the games than the anime. Even then, the manga doesn't follow the same story line the game does, it only uses the same characters.
In "The Electric Tale of Pikachu", there are some aspects that appear in the anime (around the Orange Island episodes), but it's more that the manga was based on the anime, not the other way around.
There have also been manga adaptations of Movies, e.g. the Mewtwo Movie. The Pokemon franchise is the reverse of other anime/ manga series; it goes from animation to manga.
It's also the case that the manga is pretty obscure to most English readers; there are a lot of things deemed "inappropriate" for PG-13 rating, so a lot of the manga has never been translated (officially) into English. On top of this, there are many different series for the Pokemon manga, not all of them having Ash/ Red as their main protagonist.
So ultimately, when you see a manga that has the same story line/ characters/ aspects as the anime, it's more likely that the manga was based on the anime, not the other way around.
List of Pokemon Manga
Also, Gamefreak have nothing to do with the anime; they make the games for Nintendo.
