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veg
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flea-pipeline
A pipeline for long-read sequencing data.
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Benchmark each task
#39
kemaleren
closed
9 years ago
0
Alignment-free cluster consensus
#38
kemaleren
closed
7 years ago
0
Provide alignment diagnosis to the web app
#37
kemaleren
closed
7 years ago
0
More informative diagnosis summaries
#36
kemaleren
closed
7 years ago
0
Upgrade dependencies in virtual environment.
#35
kemaleren
opened
9 years ago
1
poly-A trimming needs to check for empty sequences
#34
kemaleren
closed
9 years ago
2
Integrate alignment diagnosis
#33
kemaleren
closed
9 years ago
0
run_info.json contains strings, not json objects
#32
kemaleren
closed
9 years ago
1
Add a different walltime for long-running tasks.
#31
kemaleren
closed
9 years ago
0
HyPhy scripts fail if fasta record has a name or description
#30
kemaleren
closed
9 years ago
0
Frequencies need to be weighted by copy number
#29
kemaleren
closed
9 years ago
0
Shift correction should introduce Ns, not Xs.
#28
kemaleren
closed
9 years ago
0
replace stop codons before running HyPhy scripts
#27
kemaleren
closed
9 years ago
3
Ensure reference db does not contain stop codons
#26
kemaleren
closed
9 years ago
0
filter by length after shift correction
#25
kemaleren
closed
9 years ago
0
Shift correction improvements
#24
kemaleren
closed
7 years ago
1
poly-A filtering step
#23
kemaleren
closed
9 years ago
1
Better names for consensus sequences
#22
kemaleren
closed
9 years ago
0
usearch identity ignores terminal gaps
#21
kemaleren
closed
9 years ago
2
Make fastq file specification more user-friendly
#20
kemaleren
closed
9 years ago
0
MRCA may not be in-frame
#19
kemaleren
closed
9 years ago
1
Analysis-only pipeline needs copynumber file
#18
kemaleren
closed
9 years ago
0
Summarize flow of sequences through the pipeline
#17
kemaleren
closed
7 years ago
1
Do not run tasks on the master node
#16
kemaleren
closed
9 years ago
0
Update turnover script
#15
kemaleren
closed
9 years ago
2
HyPhy scripts rely on parsing copynumber from name
#14
kemaleren
closed
9 years ago
1
Use homology modeling to generate envelope structure
#13
kemaleren
closed
7 years ago
0
HyPhy and fasttree subpipelines do not play well together.
#12
kemaleren
closed
9 years ago
0
Root ML tree at MRCA.
#11
kemaleren
closed
9 years ago
1
Finalize data file formats.
#10
kemaleren
closed
7 years ago
0
Merge HyPhy and fasttree subpipelines
#9
kemaleren
closed
9 years ago
0
MRCA looks wrong in UMASS short dataset
#8
kemaleren
closed
9 years ago
2
Make shift correction codon-aware
#7
kemaleren
closed
9 years ago
1
Define Julia dependencies
#6
stevenweaver
closed
9 years ago
0
mafft-fftns binary should be defined in config
#5
stevenweaver
closed
7 years ago
1
copynumber task not waiting for its dependencies
#4
kemaleren
closed
9 years ago
1
Ensure pipeline generated files are created in the data directory
#3
stevenweaver
closed
9 years ago
0
wrong number of columns in rates.json
#2
kemaleren
closed
9 years ago
0
obtainEvolutionaryHistory.bf segfaults
#1
kemaleren
closed
7 years ago
3
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