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AmpliconSuite
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AmpliconSuite-pipeline
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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Guidance on creating reference genome files for a new species
#61
YxZhang-XHCY
opened
1 week ago
2
Pipeline stalling at plotting SV view
#60
at10101
closed
1 week ago
4
An error with MOSEK call in AmpliconArchitect.py
#59
carrie1s
opened
1 month ago
8
stuck in SV plotting even set--runmode as `- CYCLES`
#58
Serene0503
opened
1 month ago
6
Shared project email notification not sending on prod
#57
jluebeck
closed
2 months ago
0
How to understand different results of AmpliconArchitect in different servers?
#56
JFanbio
opened
2 months ago
5
how the pipeline generate CNV_CALLS_pre_filtered.bed file?
#55
JFanbio
closed
1 month ago
8
There are some small bugs in singularity running scripts
#54
panxiaoguang
closed
1 week ago
2
interchange between species A and B in data repo
#53
Shuixin-Li
closed
3 months ago
2
AttributeError: module 'pomegranate' has no attribute 'NormalDistribution'
#52
Tina04021997
closed
4 months ago
2
run Ampliconsuite-pipeline on WGBS data
#51
QLZhouBio
opened
5 months ago
8
Amplicon Classifier error in grouped analysis mode using mamba installed pipeline
#50
bweasels
closed
5 months ago
5
Unstable dev
#49
jluebeck
closed
6 months ago
0
Update GUIDE.md
#48
jluebeck
closed
6 months ago
0
cycle view
#47
eesiribloom
opened
7 months ago
1
Update install.sh
#46
auberginekenobi
closed
7 months ago
3
Support for non-human species
#45
Chao-Guo-hub
closed
8 months ago
4
Handling BAMs aligned with BWA-MEM -m flag
#44
tjbencomo
closed
11 months ago
2
Request for benchmarking dataset
#43
aarthi-mohan
closed
7 months ago
4
cnv_prefilter
#42
uretaj
opened
11 months ago
2
Version mismatch between Git Clone and Docker.
#41
iamyingzhou
closed
1 year ago
9
Directory issue
#40
uretaj
closed
11 months ago
6
Suggestions for arguments to AA to tweak?
#39
tischfis
opened
1 year ago
1
add samtools_path
#38
solo7773
closed
1 year ago
0
Add custom samtools
#37
solo7773
closed
1 year ago
1
Missing seed_trimmer.py in the scripts directory
#36
solo7773
closed
1 year ago
2
Long run time with *_CNV_CALLS_pre_filtered.bed
#35
WeijiaSu
opened
1 year ago
4
ValueError: cannot convert float NaN to integer
#34
WeijiaSu
closed
1 year ago
12
b37 reference genome
#33
yliu34
closed
1 year ago
5
CNVKit encountered a non-zero exit status. Exiting...
#32
jingydz
closed
1 year ago
7
please update ampliconarchitect docker image
#31
ryao-mdanderson
closed
1 year ago
10
In most runs AA_CNV_SEEDS.bed files are empty
#30
Yumo-Xie
opened
1 year ago
7
IndexError: list index out of range
#29
Cathy94
closed
1 year ago
9
changes to merge GPN container with Jens' container
#28
edwin5588
closed
1 year ago
0
AA error in insert_sdevs
#27
Tina04021997
closed
1 year ago
4
some suggestions
#26
panxiaoguang
opened
1 year ago
2
Docker permissions
#25
MrDotOne
opened
1 year ago
18
empty AA_CNV_SEEDS.bed file
#24
gneedle1
closed
1 year ago
4
less number break points
#23
sarmadmehmood89
closed
1 year ago
2
Bump numpy from 1.16.6 to 1.21.0 in /docker/requirements
#22
dependabot[bot]
closed
2 years ago
0
reference genome path
#21
gneedle1
closed
1 year ago
1
Dependency regex no longer supports python 2
#20
auberginekenobi
closed
2 years ago
1
mm10 files in data_repo are missing
#19
danielagerovska
closed
2 years ago
7
broken scripts
#18
davidhoover
closed
2 years ago
1
Always stuck at "Plotting SV View"
#17
notchw
closed
2 years ago
6
TypeError: 'NoneType' object is not callable
#16
zhangheng43
closed
2 years ago
16
Code for parsing a _cycles.txt file from AA and formatting as .bedpe
#15
auberginekenobi
closed
2 years ago
0
Parameter for cnvkit in Readme need change
#14
Si-Nan
closed
3 years ago
1
run_paa_script.sh in Docker has permission problem to write
#13
Si-Nan
closed
3 years ago
1
[AmpliconArchitect] MD tag not present
#12
zhang919
closed
3 years ago
8
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