bhattlab / phanta

Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes

bhattlab/phanta Issues

Most taxa have no taxonomy name at species level
Closed 3 months ago4
Add new vOTUs databases from other sampling compartments
Closed 5 months ago5
Memory mapping and clarification of sequencing depth reccomendations
Updated 7 months ago1
Issue with Sample File
Closed a year ago9
Question about human-infecting viruses
Closed a year ago1
[ICTV taxonomy] New taxonomy on the database
Updated a year ago1
Question about the database species
Closed a year ago3
Question of reads mapped
Closed a year ago2
The library fna file
Closed a year ago4
Environment file
Closed a year ago2
How to run it using SLURM
Closed a year ago4
Filter out host/contaminant genome?
Closed a year ago2
The question of Refseq id
Closed a year ago2
Family level is missing for some viruses
Closed a year ago2
questions of ANI & True positive
Closed a year ago4
Other link for DB?
Closed a year ago2
Testing installation using demo
Closed a year ago23
The information of database used
Closed a year ago3
Test My Installation
Closed a year ago8
I encountered a problem running Snapmake ‘snakemake: error: unrecognized arguments: --max-threads’
Closed a year ago4
PHANTA fails on single sample because `prep_to_merge_normed.py` expects header
Closed a year ago3
Consider hosting databases/datasets on alternative provider
Closed 2 years ago5
Request: Use snakemake standard resources for better portability
Closed 2 years ago2
Clarification on HumGut taxonomy
Closed 2 years ago5
Unique Permutation Warning Requires Manual Input
Closed 2 years ago2
DB cannot be loaded
Closed 2 years ago2
Add license
Closed 2 years ago
interrupted DB download
Closed 2 years ago6
Question on documentation: testin the pipeline
Closed 2 years ago3