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As I've been working on #549 to add support for SARS-CoV-2 references, I've had some trouble with running out of memory. I think it's partly that I'm running on equipment with less memory than I usual…
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Hi, I was wondering if there was any way to parse the NCBI Sequin tbl format? It is defined here: https://www.ncbi.nlm.nih.gov/projects/Sequin/table.html
I don't _think_ I see any parser for it bu…
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Hi,
I was wondering if there was going to be a new DADA2-formatted GreenGenes database based on the new release (https://forum.qiime2.org/t/introducing-greengenes2-2022-10/25291)? I was looking thr…
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### Setup
```
import sys; print(sys.version)
3.6.10 |Anaconda, Inc.| (default, Jan 7 2020, 21:14:29) [GCC 7.3.0]
import platform; print(platform.python_implementation()); print(platform.platform(…
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Migrated from https://redmine.open-bio.org/issues/3396
@olgabot said:
> As of BioPython 1.59, if an alignment is read in with Bio.AlignIO(handle, 'emboss'), the metadata such as the substitution mat…
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Biopython 1.79, pairwise2 alignment with the following two sequences runs forever:
seqA = 'ATGAGACCATCAATACCTCTTGACTATGCTCTCTTCCAACTCTCCCCAAAGCGGTCAAGATGTGAATTGTTTGTCTCTACTGCGGGGTATACTGAGAAGATT…
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tl;dr Yay ANI! https://github.com/sourmash-bio/sourmash/pull/1967 Boo ANI on translated sequences unless max_containment used :(.
Longer backstory:
For translated DNA x protein, we will have man…
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I've been having some trouble simulating HiC reads, and after an hour of troubleshooting I think I've identified the issue.
This is the command I've been running, and the error I've been running in…
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Hi,
I am a new user of PhyloSuite, I tried to download nucleotide sequences from NCBI, but it does not work. The pop-up window is: The search failed for some of the sequences. As this may have been …
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Hi everybody,
I am doing a functional metagenomic study. I did the annotation of protein sequences using HMMER against the Resfam database.
I mean I have a list of predicted resistance genes from …