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pirovc / ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
https://pirovc.github.io/ganon/
MIT License
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how to know which reads align to which bins? #206

Closed zgzg1197 closed 2 years ago

zgzg1197 commented 2 years ago

I want to know which reads are classified to which species ,can I see the reads alignment infomation?such as the bins ID ,and reads' substring which match the bin?

pirovc commented 2 years ago

Not sure if I got what you want but in ganon you get species classification but not the alignment of the read to the specific position. You could also get a classifcation at a more specific level (see specialization).

zgzg1197 commented 2 years ago

I have saw specialization ，but it is not my want (maybe i understand something wrong). Specialization classified species at higher rank ,such as spider belongs to arthropod ? But it not my want. I want to know which reads ,or subsequences like AAAA,AAAT,AAAC are classified in a bin . I want to know the groups base pair information.

pirovc commented 2 years ago

I don't quite get it what you want to do. Maybe give me an example?