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Issues list

Using standard ONT reads as ONT UL reads with the -nano option
#325 opened Mar 22, 2025 by wjhlang updated Mar 27, 2025
1
How to Generate a Pore-C Heatmap from a Verkko Assembly
#324 opened Mar 19, 2025 by fry-band updated Mar 20, 2025
2
Questions related to interpretation results phased assembly.
#245 opened Apr 5, 2024 by rfinkers updated Jan 12, 2025
@Dmitry-Antipov
54
Unmapped Region in Y Chromosome Assembly Using Verkko
#311 opened Jan 2, 2025 by LeoHongboWANG updated Jan 3, 2025
3
The --paths option can re-run the pipeline when initial asm or input file timestamps are updated
#308 opened Dec 11, 2024 by skoren updated Jan 2, 2025
5
Producing dual assemblies when no trio or Hi-C data is available enhancement New feature or request
#157 opened Jun 16, 2023 by smkumaill updated Nov 7, 2024
@Dmitry-Antipov
7
2 chromosomal fusions from verkko 2.2 assembly not supported by the data
#294 opened Oct 16, 2024 by tbenavi1 updated Nov 6, 2024
11
Homogenize trio vs hic architecture enhancement New feature or request
#197 opened Sep 28, 2023 by skoren updated Oct 21, 2024 v2.3
1
Snakemake 8 compatibility enhancement New feature or request
#224 opened Jan 13, 2024 by tbenavi1 updated Oct 21, 2024 v2.3
2
Strange GFA outputs in uncompressed gfa
#199 opened Sep 28, 2023 by skoren updated Oct 21, 2024 v2.3
Hi-C plus Trio on same run enhancement New feature or request
#193 opened Sep 15, 2023 by Dmitry-Antipov updated Oct 21, 2024 v2.3
@Dmitry-Antipov
2
Incorporate mer counting for haplotypes in verkko enhancement New feature or request
#120 opened Jan 9, 2023 by skoren updated Oct 21, 2024 v2.3
@brianwalenz
Better error reporting
#228 opened Feb 1, 2024 by Dmitry-Antipov updated Oct 9, 2024
@brianwalenz
2
Likely incorrect ONT-based resolution
#190 opened Sep 12, 2023 by skoren updated Jun 24, 2024
@maickrau
Potential graphaligner/resolution instability bug Something isn't working
#176 opened Jul 24, 2023 by skoren updated May 21, 2024
@maickrau
3
Improve coverage estimations for repeats
#172 opened Jul 13, 2023 by Dmitry-Antipov updated Jul 13, 2023
Snakemake memory allocation bug Something isn't working
#125 opened Feb 13, 2023 by steven-solar updated Jun 23, 2023
@brianwalenz
1
Identify homopolymers-count variants question Further information is requested
#7 opened Nov 5, 2021 by skoren updated Feb 17, 2023
2
Miscellaneous snakemake cleanup
#115 opened Nov 25, 2022 by skoren updated Nov 28, 2022
@brianwalenz
1
Use only patch subsequence of ONT read in consensus enhancement New feature or request
#68 opened May 3, 2022 by skoren updated Jul 19, 2022
1
Consider alternate resolution in complex tangles enhancement New feature or request
#5 opened Nov 5, 2021 by skoren updated Dec 10, 2021
Consider multiplicities of original nodes in the final layout question Further information is requested
#13 opened Nov 13, 2021 by snurk updated Nov 13, 2021
@snurk
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