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long-read-giraffe-experiments
Experimental materials for testing the long-read mapping abilities of vg giraffe
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Collect speed results, sim accuracy results, and real calling results for Giraffe all together
#54
adamnovak
opened
2 weeks ago
0
Evaluate HiFi DV accuracy after training
#53
adamnovak
opened
2 weeks ago
0
Stop tracking provenance specifically when measuring speed
#52
adamnovak
opened
1 month ago
0
Investigate if graph alignments of nanopore reads that get long softclips at surjection are correct
#51
adamnovak
opened
2 months ago
2
Upgrade to HPRC Year1-3 data
#50
adamnovak
opened
2 months ago
0
Set up minimap2 hifi variant calling and evaluation control
#49
adamnovak
closed
1 month ago
2
Make non-chaining codepath as fast as it used to be
#48
adamnovak
closed
2 weeks ago
2
Fix CHM13 HiFi reads that minimap2 gets right and Giraffe gets wrong
#47
adamnovak
opened
2 months ago
0
Improve MAPQs on HiFi reads
#46
adamnovak
opened
2 months ago
1
Evaluate performance on centromeres that are in the graph, using CHM13 reads
#45
adamnovak
closed
2 weeks ago
2
Get MAPQs from GraphAligner
#44
adamnovak
closed
2 weeks ago
1
Stop surjected nanopore reads from unmapping
#43
adamnovak
closed
2 months ago
1
Regression-test non-chaining short read codepath
#42
adamnovak
closed
2 months ago
0
Evaluate mapping to centromeres using CHM13 reads
#41
adamnovak
closed
2 weeks ago
1
Simulate CHM13 reads for evaluating centromeres
#40
adamnovak
closed
2 months ago
1
Fix HiFi reads that mismap due to increased exploration of chains
#39
adamnovak
opened
3 months ago
0
Figure out and fix HiFi reads that Giraffe leaves unmapped even on the R10 preset
#38
adamnovak
closed
3 months ago
0
Add an experiment for sampled graphs
#37
xchang1
closed
3 months ago
0
Profile and optimize parameters for R10 to get good speed without reducing accuracy or increasing unaligned bases
#36
adamnovak
closed
3 months ago
1
Work out why Banded Global Aligner middles are slow on Illumina reads
#35
adamnovak
opened
4 months ago
0
Work out why the fragment stage is slow on Illumina reads
#34
adamnovak
opened
4 months ago
0
Speed and memory
#33
xchang1
closed
3 months ago
0
performance of vg inject
#32
netwon123
opened
4 months ago
0
Make the .W indexes actually minimizer-weighted
#31
adamnovak
closed
4 months ago
0
Fix HiFi high MAPQ precision regression
#30
adamnovak
closed
4 months ago
1
Make sure we have sufficient (~30x) coverage of real reads stored for haplotype sampling
#29
adamnovak
closed
4 months ago
0
Change from "HiFi" sample to real HG002 HiFi reads
#28
adamnovak
closed
4 months ago
2
Try one-base seed anchors
#27
adamnovak
closed
2 weeks ago
1
Do variant calling on lr-giraffe Illumina reads and evaluate it
#26
adamnovak
opened
4 months ago
0
Debug duplicate chains in R10 reads
#25
adamnovak
closed
4 months ago
1
Optimize minimizer count extra parameter
#24
adamnovak
closed
2 months ago
1
Test on variant graphs from vg construct
#23
benedictpaten
opened
4 months ago
0
Fix R10 softclips again
#22
adamnovak
closed
3 months ago
0
Port paired end logic for sr code path
#21
benedictpaten
opened
4 months ago
0
Compare R9 and R10 performance with R10 preset
#20
adamnovak
closed
4 months ago
2
Produce summary performance plots for R10 and Hifi
#19
adamnovak
opened
4 months ago
0
Investigate and characterize memory usage
#18
adamnovak
opened
4 months ago
1
Look at R10's low relative numbers of mapQ 60 reads
#17
adamnovak
closed
4 months ago
1
Optimize Q27 mapping parameters
#16
adamnovak
closed
4 months ago
1
Optimize R10 mapping parameters
#15
adamnovak
closed
4 months ago
0
Use optimal Minimap2 parameters
#14
adamnovak
closed
2 weeks ago
3
Long read support for vg surject
#13
adamnovak
opened
4 months ago
0
Debug haplotype sampling with long read Giraffe
#12
adamnovak
opened
4 months ago
1
Get DeepVariant working with long read Giraffe output
#11
adamnovak
closed
2 weeks ago
0
Create haplotype sampling + variant calling long read Giraffe WDL
#10
adamnovak
closed
2 weeks ago
2
Improve WFA speed
#9
adamnovak
closed
4 months ago
0
Re-optimize HiFi parameters using improved WFA
#8
adamnovak
closed
4 months ago
1
Present long read Giraffe to HPRC call
#7
adamnovak
closed
2 weeks ago
1
Long Read Giraffe Release
#6
adamnovak
opened
4 months ago
0
Add Q27 nanopore reads to experiment
#5
adamnovak
closed
4 months ago
0
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