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Microbial-Ecology-Group
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AMRplusplus
AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
https://www.meglab.org/
GNU General Public License v3.0
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Update instructions on how to modify parameters: use --host instead of --reference.
#49
patriciatran
opened
2 days ago
0
Silent bug in host removal functions
#48
patriciatran
opened
2 days ago
0
MicrobiomeAnalysis directory empty in standard_AMR_wKraken pipeline
#47
tgaire
opened
1 week ago
0
Added apptainer to -profile
#46
Swindle98
opened
1 week ago
0
SNP verification module
#45
Jingle-H
opened
2 months ago
0
Can I run AMR++ on fasta files only?
#44
rbtoscan
opened
2 months ago
0
Error in runqc in standard_AMR pipeline
#43
pratibha-kadam
opened
3 months ago
0
Way to extract reads or read IDs related to the SNPconfirmed_deduped genes?
#42
anw-sh
opened
3 months ago
0
Error while running test file
#41
SelfShubham
opened
3 months ago
1
Analyzing Multiple Files Simultaneously with AMR++
#40
FarzanehRah
opened
3 months ago
4
Hits - How do you count?
#39
ulrichmarkus
opened
4 months ago
0
MultiQC problem - causing pipeline to fail
#38
ahayyes
opened
5 months ago
1
Fail to open file 'null' when running rm_host using slurm.sh
#37
ReedGigabyte
closed
5 months ago
1
Reporting bug of nextflow run main_AMR++.nf --help command
#36
bioinfogini
opened
5 months ago
0
The pipeline seems not really supports nextflow and slurm.
#35
nttg8100
opened
6 months ago
0
TypeError with certain samples
#34
nsharp2
opened
9 months ago
0
Using long-read data
#33
microbemarsh
opened
11 months ago
0
rename default multiqc report output (Fixes #31)
#32
stalbrec
closed
5 months ago
0
Multiqc problem/error
#31
cbryansantos
closed
5 months ago
4
RPKM
#30
dnlrxn
opened
1 year ago
0
installation
#29
BergianteGabi
opened
1 year ago
1
Latest NumPy version breaks kraken2_long_to_wide.py
#28
passdan
closed
1 year ago
2
broken link
#27
abissett
closed
1 year ago
1
Resistome
#26
GKerdivel
opened
1 year ago
1
Terms of Use
#25
GKerdivel
closed
1 year ago
1
hotfix for erorr with process tag
#24
EnriqueDoster
closed
1 year ago
0
Two errors with v3.0.3
#23
Isabella136
closed
1 year ago
3
Host rm change to samtools, name handling
#22
EnriqueDoster
closed
1 year ago
0
SNP broken in AMRplusplus
#21
CarstenBaker
closed
1 year ago
2
resistome analyzer, coverage threshold, how are mismatches handled?
#20
jessmewald
closed
1 year ago
1
Error when running AMR++(v3.0.1)
#19
priscillaisaac98
closed
8 months ago
2
Error when running with own reads
#18
mdhfz89
closed
8 months ago
6
Dev
#17
EnriqueDoster
closed
1 year ago
0
Cannot find reads
#16
felipemachado85
closed
1 year ago
11
pipeline demo crashes when parsing nextflow.config
#15
asogg
closed
1 year ago
5
Why is chr21 chosen for human read removal?
#14
tjdallman
closed
1 year ago
1
Error executing process > 'FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_R1)
#13
priscillaisaac98
closed
1 year ago
2
Error when establishing singularity version
#12
Peter-Kille
closed
1 year ago
1
Module compilation error for test data
#11
ellyyuyang
closed
1 year ago
1
Samples are failing at runsnp step of AMR++
#10
LLansing
closed
1 year ago
2
SNPConfirmed matrix contains blank column in from AMR++ run
#9
LLansing
closed
1 year ago
2
qw
#8
33353199
closed
1 year ago
1
error
#7
Hope0713
closed
1 year ago
1
not working with "real" samples
#6
pedres
closed
1 year ago
5
## cannot find nf-functions.nf module
#5
EorgeKit
closed
1 year ago
2
Unable to parse nextflow config file
#4
shreya1singh728
closed
1 year ago
36
Parsing of nextflow.config crash
#3
aghozlane
closed
1 year ago
3
runsnp failing
#2
LLansing
closed
2 years ago
5
Fix syntax error: replace '-' with '='
#1
LLansing
closed
1 year ago
1