Thomas Roder

gfapy.error.NotFoundError: A link equivalent to ... does not exist

1

Dear Giorgio Thanks for your nice library! I get this exception: ``` gfapy.error.NotFoundError: A link equivalent to: L edge_2 - edge_1 + * does not exist, but is required by...

Inconsistency between assembly_graph.gfa and assembly.fasta

4

Dear Mikhail `contig_3` in `assembly_graph.gfa` is missing in `assembly.fasta`: ```shell $ grep ">" assembly.fasta >contig_1 >contig_2 ``` Preview of `assembly_graph.gfa`: ``` H VN:Z:1.0 S edge_1 TATTTTATGAAAGAGGTGATTTTTATGCCGAAAAGA... (54kb) dp:i:1494 S edge_2...

Dear Anton LJA crashed for [this dataset](https://cloud.bioinformatics.unibe.ch/index.php/s/LCZoDsDqpg5JBQk?path=%2Fbc2130--bc2130). It's only a small bacterial genome dataset (151 MB). What is odd is that it works if I set `-o out`, but not...

Fedora 41: nothing provides libcrypto.so.1.1 and libssl.so.1.1

1

Thanks for your work! Unfortunately, on Fedora 41, the package cannot be installed: ```bash $ sudo dnf copr enable atim/spotify-tui -y && sudo dnf install spotify-tui [sudo] password for thomas:...

feat(svg): Add --render-text option for native SVG text elements

2

**Description:** This pull request introduces a new command-line option, `--render-text`, to control how node labels are rendered in the SVG output generated by BandageNG. **Motivation:** I want to make the...

Feature Request: Add Data Attributes to SVG Elements for Interactivity

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### Feature Request: Add Data Attributes to SVG Elements for Interactivity Thanks for making BandageNG, I like it a lot! However, the current SVG output lacks identifiers for the graphical...

[Request An Update]: Canu 2.3

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### What container needs an update? Thanks for your great work. Please update Canu 2.3 (Dec 17, 2024): https://github.com/marbl/canu/releases/tag/v2.3

Stupid question: nucleotide sequences

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Dear FAMSA2 developers Thanks for your great tool! I'm happily using it for large protein sequence datasets. It is never stated explicitly, but I suppose FAMSA2 is not made for...

Dear Anton I discovered that sometimes (very rarely), LJA outputs contigs duplicated contig headers: **FASTA**: ``` >1 GCAGCGAATGGCTGCGGTTTCACC... (864,307 bp) >1 GCAGCGAATGGCTGCGGTTTCACC... (858,630 bp) >5 CGGTGCCCAGCAGCTCGCCGGTGT... (1,244,402 bp) >6 AGGATGCGCCCATAGGTGCCGTCG......