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GijsBakker
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VVODKA
A tool made to create dot plots of genomes
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Error on emales example
#49
thackl
closed
1 year ago
1
Update the DOCOPT to be easier to use
#48
GijsBakker
opened
1 year ago
0
Use tool used in paper
#47
GijsBakker
opened
1 year ago
0
User MUMmer
#46
GijsBakker
opened
1 year ago
0
Reduce plot resolution to be specified by the user
#45
GijsBakker
opened
1 year ago
0
use minimap2 on data
#44
GijsBakker
opened
1 year ago
0
look into existing tools
#43
GijsBakker
opened
1 year ago
0
Get a genome for which the existing tools produce a unwanted plot
#42
GijsBakker
opened
1 year ago
0
Check for inverted not reverse
#41
GijsBakker
opened
1 year ago
0
Write a graduate planning
#40
GijsBakker
opened
1 year ago
0
Create graduation planning
#39
GijsBakker
opened
1 year ago
0
Find way to write plot in line
#38
GijsBakker
opened
1 year ago
0
Add threshold to how many kmers need to overlap within length L
#37
GijsBakker
opened
1 year ago
0
Change find match to find a sequence of matching kmers of lenth L
#36
GijsBakker
opened
1 year ago
0
Save k-mers alphabetically
#35
GijsBakker
opened
1 year ago
0
Save Both sequences in k-mer lists
#34
GijsBakker
opened
1 year ago
1
Update Plot function
#33
GijsBakker
opened
1 year ago
0
Change kmer list to a dictionary to reduce memory and time
#32
GijsBakker
opened
1 year ago
2
Fix repo, unable to push
#31
GijsBakker
opened
1 year ago
0
Create save plot functionallity
#30
GijsBakker
opened
1 year ago
0
Comparing output to output by other tools
#29
GijsBakker
opened
1 year ago
0
Create a 2bit encoder Function
#28
GijsBakker
opened
1 year ago
0
implement minimizers
#27
GijsBakker
opened
1 year ago
0
make plan were to use minimizers
#26
GijsBakker
opened
1 year ago
0
apply 2bit-encoding
#25
GijsBakker
opened
1 year ago
0
research minmizers
#24
GijsBakker
opened
1 year ago
0
Research 2 bit encoding
#23
GijsBakker
opened
1 year ago
0
Speed up Code I
#22
GijsBakker
opened
1 year ago
2
Currently a lot of memory is used
#21
GijsBakker
opened
1 year ago
0
Option to force separate or combine the given fasta files
#20
GijsBakker
opened
1 year ago
1
Auto plot onself when given one sequence
#19
GijsBakker
opened
1 year ago
0
Improve log function
#18
GijsBakker
opened
1 year ago
0
Should deal with multiple sequences in one file
#17
GijsBakker
opened
1 year ago
0
Docopt option to plot against genome itself
#16
GijsBakker
opened
1 year ago
0
Update Plot function to contain names of the sequences
#15
GijsBakker
opened
1 year ago
0
Create a way to split the kmer finding algorithm in indipendend tasks in order to multiprocess those tasks
#14
GijsBakker
opened
1 year ago
0
Expand on the argument parser to deal with multi input files
#13
GijsBakker
opened
1 year ago
0
update read fasta function to work with multiple file types
#12
GijsBakker
opened
1 year ago
1
Parallel process find_kmer
#11
GijsBakker
opened
1 year ago
1
example data
#10
thackl
closed
1 year ago
0
Create TODO cards for first two weeks
#9
GijsBakker
opened
1 year ago
0
Create a function that reads Fasta Files using BioPython
#8
GijsBakker
opened
1 year ago
0
Create a K-mer Algorithm
#7
GijsBakker
opened
1 year ago
0
Create a Function that can plot the output
#6
GijsBakker
opened
1 year ago
0
Create a Docopt argument parser
#5
GijsBakker
opened
1 year ago
0
Set-up Slack
#4
GijsBakker
opened
1 year ago
0
Set-up a Python Project
#3
GijsBakker
opened
1 year ago
0
Add Thomas to the project
#2
GijsBakker
opened
1 year ago
0