vgteam long-read-giraffe-experiments issues

vgteam / long-read-giraffe-experiments

Experimental materials for testing the long-read mapping abilities of vg giraffe

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Set up shared SnakeMake output location that Adam and Xian can both run against

#66 adamnovak closed 1 week ago
1
Merge DV WDL changes back to Snakemake

#65 adamnovak closed 1 week ago
3
Attach SV calling to Snakemake?

#64 adamnovak opened 1 week ago
0
Add multiple minimap2 presets (lr:hq and tech-named one)

#63 adamnovak closed 5 days ago
1
Add haplotype sampling to Snakemake

#62 adamnovak closed 2 days ago
1
Add a target to make the One True List of Files to the Snakemake, along with experiment configs for it

#61 adamnovak opened 1 week ago
0
Evaluate DV calling on HG001 AKA NA12878 using its new assembly-based benchmark

#60 adamnovak opened 1 week ago
0
Summary Statistics Table

#59 adamnovak opened 1 week ago
0
Investigate low SV calling accuracy on the unfiltered graph

#58 adamnovak opened 1 week ago
0
Test DV calling against the HPRC Release 2 provisional graphs with the WDL

#57 adamnovak closed 1 week ago
1
Fix weirdly low DV accuracy on the unfiltered HPRC graphs

#56 adamnovak closed 1 week ago
0
Fix very high false negative rate for insertion SVs with LRG

#55 adamnovak opened 3 weeks ago
1
Collect speed results, sim accuracy results, and real calling results for Giraffe all together

#54 adamnovak opened 2 months ago
0
Evaluate HiFi DV accuracy after training

#53 adamnovak closed 1 week ago
0
Stop tracking provenance specifically when measuring speed

#52 adamnovak closed 2 days ago
0
Investigate if graph alignments of nanopore reads that get long softclips at surjection are correct

#51 adamnovak opened 4 months ago
2
Upgrade to HPRC Year1-3 data and Release 2 graphs

#50 adamnovak closed 2 days ago
2
Set up minimap2 hifi variant calling and evaluation control

#49 adamnovak closed 3 months ago
2
Make non-chaining codepath as fast as it used to be

#48 adamnovak closed 2 months ago
2
Fix CHM13 HiFi reads that minimap2 gets right and Giraffe gets wrong

#47 adamnovak opened 4 months ago
0
Improve MAPQs on HiFi reads

#46 adamnovak opened 4 months ago
1
Evaluate performance on centromeres that are in the graph, using CHM13 reads

#45 adamnovak closed 2 months ago
2
Get MAPQs from GraphAligner

#44 adamnovak closed 2 months ago
1
Stop surjected nanopore reads from unmapping

#43 adamnovak closed 4 months ago
1
Regression-test non-chaining short read codepath

#42 adamnovak closed 4 months ago
0
Evaluate mapping to centromeres using CHM13 reads

#41 adamnovak closed 2 months ago
1
Simulate CHM13 reads for evaluating centromeres

#40 adamnovak closed 4 months ago
1
Fix HiFi reads that mismap due to increased exploration of chains

#39 adamnovak opened 4 months ago
0
Figure out and fix HiFi reads that Giraffe leaves unmapped even on the R10 preset

#38 adamnovak closed 4 months ago
0
Add an experiment for sampled graphs

#37 xchang1 closed 5 months ago
0
Profile and optimize parameters for R10 to get good speed without reducing accuracy or increasing unaligned bases

#36 adamnovak closed 5 months ago
1
Work out why Banded Global Aligner middles are slow on Illumina reads

#35 adamnovak opened 5 months ago
0
Work out why the fragment stage is slow on Illumina reads

#34 adamnovak opened 5 months ago
0
Speed and memory

#33 xchang1 closed 5 months ago
0
performance of vg inject

#32 netwon123 opened 5 months ago
0
Make the .W indexes actually minimizer-weighted

#31 adamnovak closed 5 months ago
0
Fix HiFi high MAPQ precision regression

#30 adamnovak closed 5 months ago
1
Make sure we have sufficient (~30x) coverage of real reads stored for haplotype sampling

#29 adamnovak closed 5 months ago
0
Change from "HiFi" sample to real HG002 HiFi reads

#28 adamnovak closed 5 months ago
2
Try one-base seed anchors

#27 adamnovak closed 2 months ago
1
Do variant calling on lr-giraffe Illumina reads and evaluate it

#26 adamnovak opened 5 months ago
0
Debug duplicate chains in R10 reads

#25 adamnovak closed 5 months ago
1
Optimize minimizer count extra parameter

#24 adamnovak closed 4 months ago
1
Test on variant graphs from vg construct

#23 benedictpaten closed 1 week ago
1
Fix R10 softclips again

#22 adamnovak closed 5 months ago
0
Port paired end logic for sr code path

#21 benedictpaten opened 6 months ago
0
Compare R9 and R10 performance with R10 preset

#20 adamnovak closed 6 months ago
2
Produce summary performance plots for R10 and Hifi

#19 adamnovak opened 6 months ago
0
Investigate and characterize memory usage

#18 adamnovak closed 1 week ago
1
Look at R10's low relative numbers of mapQ 60 reads

#17 adamnovak closed 6 months ago
1