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NEAT
NEAT (NExt-generation Analysis Toolkit) simulates next-gen sequencing reads and can learn simulation parameters from real data.
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variants struct
#133
joshfactorial
opened
5 days ago
0
Error with reference when running NEAT
#132
yaroslovakia
opened
1 week ago
1
130 neat crashes with target bed file 500 lines
#131
joshfactorial
closed
3 weeks ago
0
neat crashes with target_bed file > 500 lines
#130
destinymullens
closed
3 weeks ago
9
Develop
#129
joshfactorial
closed
1 month ago
0
Fixed a bug that was causing some custom sequencing error models to e…
#128
joshfactorial
closed
1 month ago
1
read-simulator error when using error model
#127
nilchia
closed
1 month ago
2
Unable to complete the read-simulator example: IndexError, KeyError.
#126
giobus75
opened
1 month ago
15
small refactoring for Markov model in development
#125
joshfactorial
closed
2 months ago
1
Develop
#124
joshfactorial
closed
2 months ago
0
1 variants skipped: (qual filtered / ref genotypes / invalid syntax)
#123
xmy1990
opened
4 months ago
4
Error when generating variants where there is a degenerate symbol in the reference
#122
dani-ture
opened
4 months ago
6
problem with trinuc.pickle.gz in gen-mut-model
#121
nilchia
closed
1 month ago
5
Difference between v3.4 and v4.2
#120
mattbird567
closed
4 months ago
2
small readme update
#119
joshfactorial
closed
4 months ago
0
Develop
#118
joshfactorial
closed
4 months ago
0
Variants not inserted from input_variants (VCF) file provided
#117
alyssa-ab
opened
5 months ago
14
Stuck in the “Covering dataset” step when changing default read length
#116
dani-ture
closed
4 months ago
3
Develop
#115
joshfactorial
closed
4 months ago
0
Processing of off-target reference regions using target bed file
#114
dani-ture
opened
5 months ago
8
Excessive coverage bias
#113
dani-ture
closed
4 months ago
3
NEAT utilities are not working
#112
nilchia
closed
4 months ago
5
Develop
#111
joshfactorial
closed
6 months ago
0
Feature/simplifying coverage
#110
joshfactorial
closed
6 months ago
0
Develop
#109
joshfactorial
closed
6 months ago
0
Empty fastq file when running neat read-simulator + default config
#108
dani-ture
closed
6 months ago
4
bug fi
#107
joshfactorial
closed
6 months ago
0
Develop
#106
joshfactorial
closed
6 months ago
0
Conda env installs correctly but fails on poetry build step
#105
MTDouglas
closed
6 months ago
4
Reworked beds a bit, as they were not quite working correctly
#104
joshfactorial
closed
6 months ago
1
Develop
#103
joshfactorial
closed
7 months ago
0
Division by zero / cant disable target regions with discard
#102
DrinnanSante
closed
6 months ago
4
README updates
#101
joshfactorial
closed
8 months ago
0
Fixed a bug where mutation rate zero was causing some unexpected Pyth…
#100
joshfactorial
closed
8 months ago
0
Minor changes to output_file_writer
#99
keshav-gandhi
closed
8 months ago
0
Found a merge conflict
#98
joshfactorial
closed
8 months ago
0
'NoneType' object has no attribute 'quality_scores'
#97
ananya-0729
closed
8 months ago
5
Update README.md
#96
joshfactorial
closed
9 months ago
0
Feature/fixing coverage
#95
joshfactorial
closed
9 months ago
0
Mutations still introduced when mutation rate is 0
#94
harrytchild
closed
8 months ago
3
Rough timeline until stable release of NEAT 4
#93
wm75
closed
8 months ago
7
Added functionality for save trinucleotide
#92
keshav-gandhi
closed
8 months ago
0
Feature/compute fraglen
#91
joshfactorial
closed
1 year ago
0
Updated descriptions of the commands and small edits!
#90
keshav-gandhi
closed
11 months ago
0
Unable to run NEAT examples in the README
#89
NuriaQueralt
closed
8 months ago
10
Re evaluation of alignment bam files failed when calling with variant calling
#88
shafayetrahat
closed
6 months ago
10
Can't run read-simulator. Probably dependency problem
#87
shafayetrahat
closed
8 months ago
19
Vcf test
#86
joshfactorial
closed
1 year ago
0
Easy way to specify not to simulate indels in the mutation model?
#85
gwct
closed
8 months ago
5
Removing pybedtools dependency.
#84
keshav-gandhi
closed
1 year ago
1
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