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As you know, the NW algorithm can be customized with different costs for indels, substitutions, gap opening and gap extension. I understand everything is unit-cost in this algorithm, but is it possibl…
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Hello,
I have been using pggb for a while now and over a couple of different builds. I have been able to run it previously and can still run a previous version (pulled February 8) without seeing thi…
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In case anyone stumbles upon the same installation error, I fixed it by adding `-lrt` to line 48 in the `Makefile` as
```
all: CC_FLAGS+=-O3 -march=native -lrt #-flto -ffat-lto-objects
```
Com…
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Hi! First of all, congrats for this great tool, it's awsome. After struggling with the compilation problems with the Biosequences update, I'm trying to run the tool without compiling but I get this er…
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Hi,
I am trying to install funannotate on a server running ubuntu. Our institution doesn't allow us to use docker for "security reasons" and the conda install hangs indefinitely, so I went the mamb…
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**What should this tool do?**
This tool should count the number of differences or "point mutations" when two equal-length sequences are aligned and compared.
**Is there an existing reference imple…
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From issue #277
Color basepairs based on interpulse distances, which indicate methylation status. The interpulse distance is provided in the "ip" SAM annotation. Instead of the standard "gray" backg…
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Hi,
I'm using bismark_genome_preparation to in-silico bisulfite convert the reference genome.
```
wget ftp://ftp.ensembl.org/pub/release-90/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplev…
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As soon as ONT R10 reads are available in a stable form, new assembly configurations for those reads should be created.
This corresponds to issues [273](https://github.com/chanzuckerberg/shasta/iss…
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Dear all,
I had trouble running a prediction with updated pdb_seqres.txt files since some entries contain unusual DNA residue names, PDB code 7ooo, 7oos and 7ozz. These nucleic acids are modified res…