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NorwegianVeterinaryInstitute
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Talos
A shotgun metagenomic analysis pipeline using nextflow
BSD 3-Clause "New" or "Revised" License
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Test the effect of the confidence level with Kraken 2
#49
Thomieh73
opened
1 year ago
0
Add a tool for contamination detection and removal from metagenomic datasets
#48
Thomieh73
opened
1 year ago
0
Update multiqc yml file
#47
Thomieh73
closed
1 year ago
0
R error with plot_avgsizes process
#46
hkaspersen
opened
2 years ago
1
Issue with R when using a personal .Rprofile
#45
hkaspersen
opened
2 years ago
0
Create singularity images from conda environments
#44
Thomieh73
opened
2 years ago
2
Add instructions to create an index of the human reference genome
#43
Thomieh73
opened
3 years ago
0
Set library location for the temporary R libraries to have
#42
Thomieh73
opened
3 years ago
0
Add report creation
#41
Thomieh73
closed
3 years ago
1
iss37,modified the script to reduce the fastq data amount it is produ…
#40
Thomieh73
closed
3 years ago
0
removed coverage calculation from the script 01_run_quality_check.nf
#39
Thomieh73
closed
3 years ago
0
nonpareil takes too long when using RAW data
#38
Thomieh73
closed
3 years ago
1
Talos produces too much data. Check all process and see how to reduce the dataout.
#37
Thomieh73
closed
3 years ago
3
Add longtime to the nonpareil processes
#36
Thomieh73
closed
3 years ago
1
iss34: resolved the symlink issue, and updated the selection of the f…
#35
Thomieh73
closed
3 years ago
0
Check out why nonpareil has problem with symlinks
#34
Thomieh73
closed
3 years ago
1
updated the Talos scripts and made it workable. The pipeline is read…
#33
Thomieh73
closed
3 years ago
1
Check how R-packages can be installed using yaml
#32
Thomieh73
opened
3 years ago
0
update Talos script to make use of the new configuration settings
#31
Thomieh73
closed
3 years ago
2
Test kraken2 database with a small mock dataset
#30
Thomieh73
closed
3 years ago
1
Create script to build a database
#29
Thomieh73
closed
3 years ago
0
created a workflow to build a kraken database using different taxonom…
#28
Thomieh73
closed
3 years ago
0
added process with kraken2 to the workflow. for now it runs with the …
#27
Thomieh73
closed
4 years ago
0
updated the process_npo_files with extra text lines
#26
Thomieh73
closed
4 years ago
0
Add kraken2 classification to Talos pipeline
#25
Thomieh73
closed
3 years ago
1
create kraken2 database with host genomes
#24
Thomieh73
opened
4 years ago
1
updated nexflow script with slurm cpu settings
#23
Thomieh73
closed
4 years ago
0
added different cpu settings to the slurm configuration
#22
Thomieh73
closed
4 years ago
0
updated standard.config
#21
Thomieh73
closed
4 years ago
0
updated my profiles
#20
Thomieh73
closed
4 years ago
0
updated config files
#19
Thomieh73
closed
4 years ago
0
created a seperate folder for yml files, added slurm/local config fil…
#18
Thomieh73
closed
4 years ago
0
updated readme
#17
Thomieh73
closed
4 years ago
0
updated the README.file
#16
Thomieh73
closed
4 years ago
0
updated nextflow script
#15
Thomieh73
closed
4 years ago
0
updated workflow figure
#14
Thomieh73
closed
4 years ago
0
removed mash, and replaced with hulk. Created Rscripts to process mic…
#13
Thomieh73
closed
4 years ago
0
added Hulk to test if comparable to mash
#12
Thomieh73
closed
4 years ago
0
small corrections made to the nextflow scripts
#11
Thomieh73
closed
4 years ago
0
Talos / add Rscript to process average genome size results
#10
Thomieh73
closed
4 years ago
0
Check if HULK is more appropriate to use than MASH for metagenomes
#9
Thomieh73
closed
4 years ago
1
Add bracken diversity estimation to the pipeline
#8
Thomieh73
opened
4 years ago
0
Should I add removal of optical /artificial duplicates?
#7
Thomieh73
closed
3 years ago
1
updated svg figure
#6
Thomieh73
closed
4 years ago
0
updated the Readme file with a figure showing the workflow
#5
Thomieh73
closed
4 years ago
0
added mash distance calculation for metagenomes to script 02
#4
Thomieh73
closed
4 years ago
0
added step to pipeline: average genome size calculation
#3
Thomieh73
closed
4 years ago
0
added nextflow scripts and additional files to the repo
#2
Thomieh73
closed
4 years ago
0
added nextflow configuration file
#1
Thomieh73
closed
4 years ago
0