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bhattlab
/
phanta
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
MIT License
60
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9
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Clean-up conda environment.
#46
njohner
opened
2 days ago
0
Most taxa have no taxonomy name at species level
#44
DrYoungOG
closed
2 months ago
4
Memory mapping and clarification of sequencing depth reccomendations
#43
joshuakirsch
opened
6 months ago
1
Issue with Sample File
#40
amgroth
closed
10 months ago
9
More efficient table merging
#39
alienzj
closed
11 months ago
1
[ICTV taxonomy] New taxonomy on the database
#38
rdenise
opened
1 year ago
1
Question about human-infecting viruses
#37
gazollavolpiano
closed
1 year ago
1
Add new vOTUs databases from other sampling compartments
#34
mhmism
closed
4 months ago
5
Question about the database species
#33
Iris7788
closed
1 year ago
3
Question of reads mapped
#32
wen1112
closed
1 year ago
2
The library fna file
#31
alienzj
closed
1 year ago
4
add runner script
#30
telatin
closed
1 year ago
0
Fix installation issues due to environment YAML file
#29
telatin
closed
1 year ago
0
Environment file
#28
telatin
closed
1 year ago
2
Filter out host/contaminant genome?
#27
mhmism
closed
1 year ago
2
The question of Refseq id
#25
wen1112
closed
1 year ago
2
How to run it using SLURM
#23
Sanrrone
closed
1 year ago
4
Family level is missing for some viruses
#22
Sanrrone
closed
1 year ago
2
Other link for DB?
#20
Sanrrone
closed
1 year ago
2
questions of ANI & True positive
#19
wen1112
closed
1 year ago
4
The information of database used
#18
wen1112
closed
1 year ago
3
Testing installation using demo
#17
hgingras
closed
1 year ago
23
I encountered a problem running Snapmake ‘snakemake: error: unrecognized arguments: --max-threads’
#15
JinhuiHe1
closed
1 year ago
4
Test My Installation
#14
wen1112
closed
1 year ago
8
making collapse_viral_abundances_by_host. fail gracefully if no viruses
#13
nickp60
closed
1 year ago
1
PHANTA fails on single sample because `prep_to_merge_normed.py` expects header
#12
nickp60
closed
1 year ago
3
Change to standard resource names and units
#10
nickp60
closed
1 year ago
3
Request: Use snakemake standard resources for better portability
#9
nickp60
closed
1 year ago
2
Unique Permutation Warning Requires Manual Input
#8
vzg100
closed
1 year ago
2
Consider hosting databases/datasets on alternative provider
#7
funnell
closed
1 year ago
5
DB cannot be loaded
#6
StfnRomano
closed
2 years ago
2
Clarification on HumGut taxonomy
#4
snayfach
closed
2 years ago
5
Add license
#3
snayfach
closed
2 years ago
0
interrupted DB download
#2
GaioTransposon
closed
2 years ago
6
Question on documentation: testin the pipeline
#1
telatin
closed
2 years ago
3