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dereneaton
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ipyrad
Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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Not including minmap in PCA/Structure
#463
alexkrohn
closed
2 years ago
2
Object 'quartets' does not exist
#462
alexkrohn
opened
2 years ago
4
Tetrad cannot allocate memory
#461
alexkrohn
closed
2 years ago
5
Which vcf file is more suitable for calculating SFS?
#460
zilaijuand
closed
2 years ago
2
kmeans imputation niters fix
#459
TankredO
closed
2 years ago
1
how to find out this parameters?
#458
zilaijuand
closed
2 years ago
2
Running out of Hard Drive Space: How to Predict Temp File Sizes?
#457
alexkrohn
closed
2 years ago
2
Error when run ipyrad
#456
yexiaying199056
closed
2 years ago
3
MemoryError() When Generating VCF
#455
alexkrohn
closed
2 years ago
2
ignore Ns for uSNP selection
#454
cdoorenweerd
opened
2 years ago
4
Step 7: Error 72
#453
MCampos92
closed
2 years ago
2
Message: No samples ready for step 3. If branching, use the `-f` flag to force re-running step 3.
#452
zilaijuand
closed
2 years ago
2
vcf_to_hdf5 and tetrad: 'str' object has no attribute 'decode'
#451
casparbein
closed
2 years ago
1
Message: IPyradError: bwa error: None
#450
zilaijuand
closed
2 years ago
2
vcf2hdf5
#449
pengyan19
closed
2 years ago
11
Crash at the end of step 3
#448
carlahurt
closed
3 years ago
11
AssertionError: Different number of R1 and R2 files
#447
laaryjc
closed
3 years ago
2
Fatal error: Files compressed with gzip are not supported
#446
laaryjc
closed
3 years ago
2
WIP: Notebook is already a dependency of iPyrad
#445
mikerenfro
closed
3 years ago
2
Aligning to large chromosomes
#444
carlahurt
closed
3 years ago
13
Removing individuals
#443
carlahurt
closed
3 years ago
2
overlapping loci and duplicated SNPs
#442
pdpapper
opened
3 years ago
4
Added retain boots option to ABBA-BABA module
#441
camayal
closed
3 years ago
0
Fixing mismatch of #SBATCH and command parameters
#440
mikerenfro
closed
3 years ago
1
Reference-Based assembly with reference as an output
#439
Phismil
closed
3 years ago
1
Error at step 1 with a chunk
#438
simjoly
closed
3 years ago
7
Step 3 gets to 85% and crashes.
#437
Pgjhmb
opened
3 years ago
9
Barcode file not being read, unsure if this is a params issue or a continued formatting error?
#436
konradtaube
closed
3 years ago
2
concatenating bams hangs at 66%
#435
nbedelman
closed
3 years ago
9
Could output files reflect polyploidy?
#434
ThrsBT
opened
3 years ago
2
Barcode file not being read, possibly due to formatting issue on my end?
#433
konradtaube
closed
3 years ago
1
Eaton&Ree CLI Tutorial Issue
#432
konradtaube
closed
3 years ago
11
Failed @ Step 2
#431
Pgjhmb
closed
3 years ago
2
Branching and removing samples from an assembly with pops file causes a race condition
#430
isaacovercast
closed
3 years ago
2
Step 7 - No loci pass filtering (filtered by rm_duplicates)
#429
isaacovercast
closed
3 years ago
4
cookbook empirical API 1 Pedicularis Structure is out of date
#428
isaacovercast
closed
3 years ago
2
ipyrad conda environment: sharde library
#427
ARW-UBT
closed
3 years ago
3
Expected time for step 3?
#426
rspfau
closed
3 years ago
1
baba analysis plotting in v0.9 is broken
#425
isaacovercast
closed
3 years ago
4
Problem with demultiplexing of 3RAD dataset
#424
ludmilasromek
closed
3 years ago
7
Multiple Step 2 errors
#423
aveeva
closed
3 years ago
4
Step 7: TypeError: Can't broadcast (47, 150000) -> (47, 4909)
#422
isaacovercast
closed
3 years ago
10
Feature request: min_samples_snp parameter
#421
isaacovercast
opened
3 years ago
1
baba Error - "error: {}: {}".format(job, asyncs[job].exception()))
#420
btmartin721
closed
3 years ago
5
ipyrad install on python 3.8 is broken?
#419
isaacovercast
closed
3 years ago
5
Installing problem
#418
gubrins
closed
3 years ago
1
Changed astral annotation to default
#417
camayal
closed
3 years ago
0
missing depencies in the documentation
#416
oliviermattelaer
closed
3 years ago
3
Merge exists with 1
#415
miguelpmachado
closed
3 years ago
1
analysis.pca: Impute missing as random value
#414
isaacovercast
opened
3 years ago
0
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