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I am currently performing polishing of a large eukaryotic genome (mouse) assembled with flye.
as noted in the documentation, I understand that the latest version of medaka is intended to be used d…
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The unit test 'smrt-pipeline.t' shows that there are still some random elements in the pipeline and
therefore it is difficult to reproduce results exactly with multiple pipeline runs. This becomes app…
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The FragmentStore does neither support soft nor hard clipping.
For soft-clipping, the full sequence is in the SEQ field of SAM files and the anchor gaps data structure supports clipping with anchors.…
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Hi Inigo,
I have multiple samples where Circle-Map will fail with:
`"An error happenend during execution. Exiting"`
stderr:
```
[E::idx_find_and_load] Could not retrieve index file for 'outpu…
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[[tab:meta.trans.other]](http://eel.is/c++draft/meta.trans.other#sentence-6) specifies that default-alignment in
```c++
template
struct aligned_storage;
```
"shall be the most stringent alignment…
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I work on a scheduled cluster. Sometimes my jobs time out. Rather than start fresh, I would like sortmerna to resume at the point where it was shut down.
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Suggestions provided by @haruosuz
- bactopia can accept GFF3 files (.gff) instead of FASTA files (.fna) as input, like PIRATE and Roary, to skip Prokka?
- bactopia can do alignment trimming (e.g. …
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Request that add some @amandamok's simulated ribosome profiling data into RiboViz as another vignette. This should provide ideal testing that reads are correctly aligned and of codon-level and gene-le…
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Hello!
I am processing ITS data with DADA2 (primers ITS1F-ITS2). I am following recommendations from this paper (https://www.sciencedirect.com/science/article/pii/S1754504818302800?via%3Dihub) and fo…
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First time using this package. I have run an alignment with linclust and am wondering if there is a way of extracting the positional information of the clusters and the distance between them, with the…