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genomic-medicine-sweden
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taxprofiler
Taxonomic profiling of shotgun metagenomic data
https://nf-co.re/taxprofiler
MIT License
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Fastp filtering
#43
sofstam
opened
5 months ago
0
ribodector to remove rRNA before classification
#42
LilyAnderssonLee
opened
8 months ago
2
Validate the latest versions of databases
#41
LilyAnderssonLee
opened
10 months ago
1
Report the common contaminants in routine pipeline
#40
LilyAnderssonLee
opened
10 months ago
0
Standardize the update of databases and taxonomy
#39
LilyAnderssonLee
opened
10 months ago
0
Build centrifuge db
#38
sofstam
opened
10 months ago
0
Build krakenuniq db
#37
sofstam
opened
10 months ago
0
Build centrifuge database
#36
LilyAnderssonLee
opened
1 year ago
1
(feat centrifuge) hitLength and numMatches
#35
sofstam
opened
1 year ago
0
Test KrakenUniq
#34
sofstam
opened
1 year ago
1
Construct databases for all profilers from the same input refseq data
#33
LilyAnderssonLee
opened
1 year ago
1
Test kmcp classifier
#32
sofstam
opened
1 year ago
0
Confidence score in Kraken2
#31
LilyAnderssonLee
opened
1 year ago
1
Include genomes of potential contaminants during the host-removal stage.
#30
LilyAnderssonLee
closed
1 year ago
1
Test the profiler Kaiju
#29
LilyAnderssonLee
opened
1 year ago
2
Test CENTRIFUGE with classification filterings, and compare centrifuge to Kraken2
#28
LilyAnderssonLee
opened
1 year ago
5
Test DIAMOND
#27
LilyAnderssonLee
opened
1 year ago
7
Run Kraken2 based on BLAST nt databse
#26
LilyAnderssonLee
closed
11 months ago
3
GMS-Mikro Viruspool
#25
sofstam
opened
1 year ago
0
GMS-Mikro Viruspool
#24
sofstam
closed
1 year ago
0
GMS-Mikro viruspool
#23
sofstam
closed
1 year ago
0
Test profiler ganon
#22
sofstam
opened
1 year ago
0
Update taxpasta version
#21
sofstam
closed
1 year ago
1
Update porechop module
#20
sofstam
closed
2 years ago
1
Add KrakenUniq and Filtlong in documentation
#19
sofstam
closed
2 years ago
1
kaiju/kaiju2table needs to be added to taxprofiler
#18
sofstam
closed
2 years ago
0
kaiju/kaiju needs to be added to taxprofiler
#17
sofstam
closed
2 years ago
0
centrifuge/kreport needs to be added to taxprofiler
#16
sofstam
closed
2 years ago
0
Minimap2 module needs to be updated
#15
sofstam
closed
2 years ago
1
Delete nf-core/modules/centrifuge/centrifuge directory
#14
sofstam
closed
2 years ago
0
Reads are classified with at least on of the following taxonomic profilers: kraken2/centrifuge/kaiju/metamaps #22
#13
sofstam
closed
1 year ago
0
Memory issue for bbduk and -profile test,hasta,dev_prio
#12
sofstam
closed
2 years ago
2
Test run nf-core/taxprofiler with nf-tower
#11
sofstam
closed
1 year ago
1
Complexity filtering for Nanopore data
#10
sofstam
closed
1 year ago
1
Test dataset for Centrifuge, Kaiju and MetaMaps when running the pipeline with -profile test
#8
sofstam
closed
1 year ago
1
We need to be able to run the pipeline
#6
henningonsbring
closed
2 years ago
5
Host-reads removal for Nanopore reads
#5
sofstam
closed
2 years ago
0
Preprocessing: Add porechop for Nanopore data
#4
sofstam
closed
2 years ago
2
Add MetaMaps for Nanopore
#3
sofstam
closed
1 year ago
0
Add option to use sample/control as input
#2
sofstam
closed
1 year ago
1
Add Nanopore input
#1
sofstam
closed
2 years ago
0