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When `CREATE_SCHEMA` config is disabled, the sequence export still tries to create the schema, resulting in a permission failure if the Postgres user can't create the schema. This is an issue in envir…
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## Expected Behavior
`mmseqs download` would be expected to download an up-to-date version of the target 'nr' and 'nt' databases.
## Current Behavior
The download FASTA targets for the 'nr' and '…
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This is using the statically linked, single threaded versions downloaded in the last couple of days, running on Linux.
I'm just starting with hh-suite, and trying to create a custom database. I tho…
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Hello everyone,
I building GTDB databases to be used along with Kraken2. I was wondering if it was possible to add viral refseq sequences while building kraken2 databases? GTDB consists of archaeal a…
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Whitespace between movetext tokens is not stored on a database.
This breaks for sequences like '$1 1/2-1/2' because '$11/2-1/2' is seen by the PGN parser as '$11' and '/2-1/2'.
Solution is to en…
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Hi there!
I utilized EMU to classify 16S and 18S rRNA amplicons sequenced using nanopore sequencing with the SQK-NBD114.96 kit. However, I noticed that some of the taxonomic assignments made by EMU …
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Main points:
* Expand https://github.com/pyani-plus/pyani-plus/blob/main/pyani_plus/private_cli.py with another function ``log_dnadiff`` (like the existing ``log_anim``, ``log_anib``, ``log_fastani…
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I add a special row in Taxonomy table to handle taxonomy should not be NULL situation. Its ID is 1. Tax_id is 0. Tax_id column saves the taxonomy ID from [NCBI](https://www.ncbi.nlm.nih.gov/datasets/t…
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Hi,
Is there a way to extract species-specific kmers from the database and assemble them into species-specific sequences as long as possible?
These can then be used to design diagnostic PCR primers…
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Hello
I have two viral contigs of approximately 3500bp from the same region of a genome. The two contigs differ by just 1%. Virsorter is run as:
virsorter run -w test.out -i test.fa --min-length 150…