Ryan Lorig-Roach

Allow resizing text?

2

In shasta assembly graphs, the node size range goes from 1bp all the way to 100Mbp and the font size is often too small when looking at the graph from...

Hi, I am attempting to use your example.c as a template for aligning some assembly haplotypes: https://github.com/rlorigro/GFAse/blob/0ce1fb2990bce9b0f4ab27dade77ff1263402deb/src/test/test_minimap2.cpp#L39 Target: https://github.com/rlorigro/GFAse/raw/main/data/long_challenge_node.fasta Query: https://github.com/rlorigro/GFAse/raw/main/data/short_challenge_nodes.fasta My adaptation of example.c tries to apply the the...

Forcing continuous alignments

12

Hi, I am using minimap2 to map long ONT reads (up to 400Kbp), and I am finding that the supplementary chaining is producing large rearrangements in the read sequence, flipping...

Before using the command: `gfatools view -l 303726,303738 -r 20 Assembly-BothStrands.gfa > Assembly-BothStrands_303726-303738_r20.gfa` my GFA has the following elements: ``` S 5924062 GTTTCAAAAAAAAAAAAAGAGCATGGCTCTGG RC:i:400 L 5209751 + 5924062 + 18M1D6M...

Linkable library?

1

Hi, This is super cool. I'm a researcher in bioinformatics, and we frequently need to visualize large graphs involving genome assembly data. Is there a core layout method from your...

Hi, I am cross-posting [this issue](https://github.com/at-cg/PanAligner/issues/1) which I have submitted to the PanAligner repository, since it has been found by the authors to be a result of the base-level alignment...

Hi, I am using minigraph in a local context (

Environment-dependent samtools view error (invalid BGZF header) with remote GCS BAM

8

### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib](https://github.com/samtools/htslib/releases/latest)? If not, please specify. Yes, but this error is error is environment dependent so I will list both environments:...

Homopolymer indels not consistently aligned

6

Hi, I am trying to get a reasonable alignment in a region which has some tandem repeats, flanked by non-repetitive sequence. I can get good (enough) results in the tandem...

Hi, I linked your library and I'm able to use a combination of a `KmerIterator` and your `CompactedDBG` class to query k-mers in a de Bruijn graph I have stored...