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Hello,
it seems that some sequences that are successfully aligned to the reference end up in the nt-debug folder.
While some that failed to do so are not present in the nt-debug folder.
Kind …
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It'd be nice to provide a single high-level function, e.g. `skbio.pwalign`, that gives access to the various pairwise aligners in scikit-bio (SSW aligner and @gregcaporaso's local and global aligners …
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Greetings, I'm trying to make use of MCScanX_h, i've prepared the necessaries files following the manual yet my data neither example data is working.
My gff with 5 species gff is edited follwing t…
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Need to add functionality to lift co-ordinates in one sequence over to the other sequence in pairwise alignments. This should take into account gaps, and might return more than one genomic interval if…
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Hello,
I've got a question regarding the argument `--maxaccepts` of the `vsearch` command `--cluster_fast`:
The manpage states the following about `maxaccepts`:
"_The search process sorts tar…
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Dear Hifiasm community and developers,
This is a very important piece of software. Now I'm having some problems.
How can I obtain information on All-versus-all pairwise alignment to view the ove…
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Currently the formatting of the help messages (defined via the leading docstrings at the start of each script in `augur/*.py`) is not respected by `augur --help`. We should improve this which will en…
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When running QC/QA, the first thing that is done is a pairwise alignment. The quality of this alignment can have a big impact of the result. The setting of gap score and gap extend penalties should be…
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What would be the command line parameters for `parasail_aligner` for doing local pairwise alignment (without gaps within the sequences) of two DNA sequences
For example, `1.fa` is like this
```
…