We mostly use SeqViz with genbank files and have noticed that annotation parsing is off without us being able to really figure out why/how to fix it in the files. I can try to find an example for you we can share (hard because it's mainly customer IP we're working with). But the same file in SeqViz and in Snapgene render differently and it results in both more, but wrong, annotation shown in SeqViz and fewer/hidden annotations that doesn't appear in SeqViz.
Visualisation of unassembled strains
Some of the genbank files we have contain multiple strains (typically unassembled reads), which SeqViz by default concatenates the sequences as it was one – which is wrong and hard to catch. Snapgene let's you select which of the sequences to view, which is what we've now built ourselves too, so that we add a select-step before rendering just one of the sequences in the file with SeqViz.
jjti
commented
2 years ago
Buggy annotations
We mostly use SeqViz with genbank files and have noticed that annotation parsing is off without us being able to really figure out why/how to fix it in the files. I can try to find an example for you we can share (hard because it's mainly customer IP we're working with). But the same file in SeqViz and in Snapgene render differently and it results in both more, but wrong, annotation shown in SeqViz and fewer/hidden annotations that doesn't appear in SeqViz.
Visualisation of unassembled strains
Some of the genbank files we have contain multiple strains (typically unassembled reads), which SeqViz by default concatenates the sequences as it was one – which is wrong and hard to catch. Snapgene let's you select which of the sequences to view, which is what we've now built ourselves too, so that we add a select-step before rendering just one of the sequences in the file with SeqViz.
whatever the fixes are they're go into https://github.com/Lattice-Automation/seqparse