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Hello,
I'm attempting to run a profile alignment using two sub alignments stored as string in memory. In order to do so I am initialising a new Alignment object using an iterable of GappedSequence …
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I'm using the C API of `block-aligner` to align protein sequences from UniProt database. There are `*`s in some protein sequences. Currently using `block-aligner` to align sequences containing `*` wil…
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Hey @jguhlin,
Apologies if this is a naive question: I'm wondering if there's a programmatic way to tell the mapper _not_ to allow soft-clippings, and to instead force the alignment of the ends (ev…
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Hello,
I am experiencing the following problem all of a sudden:
"100000 alignment records processed.
200000 alignment records processed.
300000 alignment records processed.
Error occured when…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
import sys; print(sys.version)
import platform; print(platform.python_imp…
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Hello!
Thanks again for your great tool. I wondering what your thoughts were on the idea of replacing BLAT/pblat with a tool like [minimap2](https://github.com/lh3/minimap2) for probe alignment.
…
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Hi,
Is it possible to have DRAGMAP report all alignments similar to BWA-MEM with the `-a` option? This seems possible with the different `sec` parameters, but I have not been able to get more than …
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Hey @Daniel-Liu-c0deb0t!
I have a bunch of sequences (most 20nts, few 27nts) which I want to find in a lot (millions) of longer sequences.
Initially I use a k-mer index, and find matching pairs…
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Input is FASTA reference. Output is the aligner index, samtools faidx and picard sequence dictionary.
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Hi Adrian,
Using an aligner such as STAR or Tophat seems to give more alignments/content from indrop sequence reads compared to the current Bowtie aligner usage. Would it be possible to incorporate…