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hoelzer
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mgnify-lr
Evaluation of long-read support for the MGnify pipeline
GNU General Public License v3.0
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Revision 2024
#49
hoelzer
closed
9 months ago
0
Dev
#48
hoelzer
closed
4 years ago
0
Dev
#47
hoelzer
closed
4 years ago
0
Lathe Snakemake pipleine for complete closed genomes from microbiome
#46
hoelzer
opened
4 years ago
0
latency problems on HPC
#45
hoelzer
closed
4 years ago
0
update dev with ideel wf
#44
hoelzer
closed
4 years ago
0
add analysis only workflow for ideel
#43
hoelzer
closed
4 years ago
0
Update dev
#42
hoelzer
closed
4 years ago
0
Add sensitive mode for polishing
#41
hoelzer
opened
4 years ago
1
fastp parameters
#40
hoelzer
closed
4 years ago
0
basedir for clean-up indices
#39
hoelzer
closed
4 years ago
0
Dev
#38
hoelzer
closed
4 years ago
0
Dev
#37
hoelzer
closed
4 years ago
0
Reorder
#36
hoelzer
closed
4 years ago
0
use nano-raw instead of nano-corr for flye v2.7
#35
hoelzer
closed
4 years ago
0
Polishing evaluation
#34
hoelzer
opened
4 years ago
2
Bbduk
#33
hoelzer
closed
4 years ago
0
pilon samtools sort HPC error
#32
hoelzer
closed
4 years ago
1
short-read decontamination with minimap2 removes a lot
#31
hoelzer
closed
4 years ago
2
estimate gsize error handling
#30
hoelzer
closed
4 years ago
1
Decontamination
#29
hoelzer
closed
4 years ago
0
Profiles
#28
hoelzer
closed
4 years ago
0
Merged Nextflow profiles
#27
hoelzer
closed
4 years ago
0
HyPo: super fast hybrid polishing
#26
hoelzer
opened
4 years ago
0
execution summary
#25
hoelzer
closed
4 years ago
0
finalize hybrid assembly approach
#24
hoelzer
closed
4 years ago
2
ideel plots
#23
hoelzer
closed
4 years ago
1
Add decontamination of basic spike-ins
#22
hoelzer
closed
4 years ago
0
Provide decontamination db directly without download
#21
hoelzer
closed
4 years ago
1
implement guess genome size as an optional parameter
#20
hoelzer
closed
4 years ago
1
Check estimation of gsize
#19
hoelzer
closed
4 years ago
1
add conda profile
#18
hoelzer
closed
4 years ago
0
SRA support
#17
hoelzer
closed
4 years ago
0
adjust ENA files for hybrid workflow
#16
hoelzer
closed
4 years ago
0
Hybrid
#15
hoelzer
closed
4 years ago
0
Add decontamination of short reads
#14
hoelzer
closed
4 years ago
1
HASLR: fast hybrid assembly
#13
hoelzer
closed
4 years ago
1
Add low abundance kmer filter before gsize estimation
#12
hoelzer
closed
4 years ago
1
Full reproducibility
#11
hoelzer
closed
4 years ago
1
estimated gsize set to 1m when below 1
#10
hoelzer
closed
4 years ago
1
output ENA project.xml file
#9
hoelzer
closed
4 years ago
1
output ENA manifest file for assembly upload
#8
hoelzer
closed
4 years ago
2
output coverage
#7
hoelzer
closed
4 years ago
1
decontamination
#6
hoelzer
closed
4 years ago
1
direct SRA access
#5
hoelzer
opened
4 years ago
1
Add basecalling support
#4
hoelzer
opened
4 years ago
1
hybrid assembly: POLCA polishing
#3
hoelzer
closed
4 years ago
3
run racon 4x
#2
hoelzer
closed
4 years ago
1
estimate gsize
#1
hoelzer
closed
4 years ago
6