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cerebis
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meta-sweeper
Parametric sweep of simulated microbial communities and metagenomic sequencing.
GNU General Public License v3.0
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A5 use of Unix "file" command is tricked by symbolic links
#79
cerebis
closed
7 years ago
2
Low coverage assemblies can return non-zero exit
#78
cerebis
opened
7 years ago
0
More recent versions of Nextflow throw exceptions with MetaSweeper.java
#77
cerebis
closed
7 years ago
1
Check sort order on contact_map.py
#76
cerebis
opened
7 years ago
0
Organisation of shared dependent modules
#75
cerebis
opened
7 years ago
0
Unintended rescaling of trans-rate
#74
cerebis
closed
7 years ago
0
Possible extension of profiles to include more definition.
#73
cerebis
opened
7 years ago
0
Implement free shearing simulation
#72
cerebis
opened
7 years ago
0
Multi-chrom genomes with procedural abundances
#71
cerebis
opened
7 years ago
0
Fine-tuning simple structure simulation by nested intervals
#70
cerebis
opened
7 years ago
1
Treatment of sparse sites and wgs read-pair noise
#69
cerebis
closed
7 years ago
4
Specifying a few resource limits might be useful.
#68
cerebis
opened
7 years ago
0
Facility for fixed, user defined tree
#67
cerebis
closed
7 years ago
2
Occasional occurence of java.util.ConcurrentModificationException
#66
cerebis
opened
7 years ago
0
Unintended continuation when single clade timeseries is given a multiple clade community
#65
cerebis
opened
7 years ago
0
snvbpnmft.py throws an error when there are no reliable variant sites.
#64
cerebis
closed
7 years ago
0
Use of JavaSE8 Map.putIfAbsent()
#63
cerebis
opened
7 years ago
0
nextflow hangs rather than exiting after workflow termination
#62
koadman
opened
7 years ago
3
params.debug undefined
#61
koadman
closed
7 years ago
5
Only two clades are used in multi-clade configurations
#60
koadman
closed
7 years ago
0
Random sampling of parameter space
#59
cerebis
opened
7 years ago
1
pipeline_utils.py is not used
#58
cerebis
closed
7 years ago
0
bash_configure not setting environment variables
#57
koadman
closed
7 years ago
3
Add documentation for satisfying beagle-lib dependency of timeseries workflow.
#56
cerebis
closed
7 years ago
1
wait_on jiffy only works for single files.
#55
cerebis
opened
7 years ago
0
test profile table no long correct format
#54
cerebis
closed
7 years ago
0
JNI_LIB_PATH should not be an explicit absolute path
#53
cerebis
closed
7 years ago
1
sim3C: consider exposing more parameters controlling empirical distribution to users
#52
cerebis
opened
7 years ago
0
3-way channel cross in multisample
#51
koadman
opened
7 years ago
1
Merge multisample into master
#50
koadman
closed
7 years ago
0
Validate poly-chromosomal genomes in sim3C
#49
cerebis
closed
7 years ago
1
Validate treatment of sim3C site duplication
#48
cerebis
closed
7 years ago
2
Adopt a space efficient graph interchange format
#47
cerebis
opened
7 years ago
4
Some naive operations possess poor time complexity.
#46
cerebis
closed
7 years ago
0
Longer read-pairs (250bp) can lead to read-through problems. Add a warning.
#45
cerebis
closed
7 years ago
5
Read creation rate of ART could be improved.
#44
cerebis
closed
7 years ago
1
sim3C should make use of a observer pattern
#43
cerebis
opened
7 years ago
0
SimForward must gracefully handle templates without cutsites
#42
cerebis
closed
7 years ago
2
Simulating sequencing reads
#41
cerebis
closed
7 years ago
0
BWA MEM mapping can produce no mapped reads to some contigs
#40
cerebis
opened
7 years ago
6
Ability to simulate simple 3D structure in Hi-C/3C reads
#39
koadman
opened
8 years ago
17
Add procedural tree and profile support to workflow
#38
cerebis
closed
7 years ago
1
simForward.py appears to have a minor defect in sample from distributions
#37
cerebis
closed
7 years ago
1
Assigning profiles within and across trees.
#36
cerebis
closed
7 years ago
3
Procedural abundance profiles
#35
cerebis
closed
8 years ago
2
Non-deterministic cache misses
#34
cerebis
closed
8 years ago
4
Cached custom objects rely on weak hash codes
#33
cerebis
closed
7 years ago
6
Nextflow resume is broken by the NamedValue helper class
#32
cerebis
closed
8 years ago
1
phylogenetic tree generation
#31
cerebis
closed
8 years ago
8
support a 'local' config outside the repo
#30
koadman
closed
7 years ago
0
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