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kapsakcj
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nanoporeWorkflow
:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
MIT License
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Workflow languages
#40
lskatz
opened
3 years ago
2
add step to re-orient medaka asms to start with dnaA
#39
kapsakcj
opened
3 years ago
0
update to latest guppy version
#38
kapsakcj
closed
3 years ago
9
racon polishing turn down scripts to use 16 max threads
#37
kapsakcj
closed
3 years ago
1
dig into Flye error - CRC check failed
#36
kapsakcj
closed
3 years ago
1
rename final medaka-polished assembly to something more obvious
#35
kapsakcj
closed
3 years ago
1
turn down medaka_consensus to --threads 8
#34
kapsakcj
closed
3 years ago
0
remove filtlong step, implement flye --asm-coverage
#33
kapsakcj
opened
3 years ago
1
use pigz in filtlong container, don't rely on hpc node
#32
kapsakcj
closed
3 years ago
1
ensure filtlong check actually works
#31
kapsakcj
closed
3 years ago
1
upgrade to NanoPlot 1.32.0
#30
kapsakcj
closed
3 years ago
3
upgrade to Guppy 4.0.11
#29
kapsakcj
closed
4 years ago
1
add socru script
#28
kapsakcj
opened
4 years ago
2
add Tiptoft for plasmid prediction
#27
kapsakcj
opened
4 years ago
0
upgrade to singularity 3.5.3?
#26
kapsakcj
closed
3 years ago
2
add print statements to nanoplot script
#25
kapsakcj
closed
4 years ago
1
add support for NB13-24 workflow-after-gpu-basecalling.sh
#24
kapsakcj
closed
3 years ago
4
fast5 file validation
#23
kapsakcj
opened
4 years ago
0
remove redundant check in racon script
#22
kapsakcj
closed
4 years ago
0
remove git-lfs requirement & alter test data format
#21
kapsakcj
opened
4 years ago
2
add optional flag for writing basecalled fast5s w/ guppy
#20
kapsakcj
opened
4 years ago
2
update links from old repo location
#19
kapsakcj
closed
4 years ago
1
fix nanoplot qsub -hjid
#18
kapsakcj
closed
4 years ago
1
add module for NanoPlot
#17
kapsakcj
closed
4 years ago
3
migrate to guppy 3.6.0 for basecalling
#16
kapsakcj
closed
4 years ago
3
fix tmpdir name in medaka script
#15
kapsakcj
closed
4 years ago
1
set filtlong to exclude reads below 500bp instead of 1kb
#14
kapsakcj
closed
4 years ago
0
fix checking in racon script
#13
kapsakcj
closed
4 years ago
1
actually add support for native barcodes 13-24
#12
kapsakcj
closed
4 years ago
0
add Pilon polishing script
#11
kapsakcj
opened
4 years ago
0
add $GENOME_LENGTH param
#10
kapsakcj
opened
4 years ago
1
update README on basecalling
#9
kapsakcj
closed
4 years ago
3
move qsub.log and qsub.err
#8
kapsakcj
closed
4 years ago
2
create /scripts/deprecated
#7
kapsakcj
closed
4 years ago
1
Curtis dev [ci skip]
#6
kapsakcj
closed
4 years ago
0
Curtis dev
#5
kapsakcj
closed
4 years ago
0
add Racon and Flye scripts...
#4
kapsakcj
closed
4 years ago
1
Curtis dev
#3
kapsakcj
closed
5 years ago
0
Curtis dev
#2
kapsakcj
closed
5 years ago
0
merge Curtis dev branch
#1
kapsakcj
closed
5 years ago
2