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Hello Kraken team,
I am analysing shotgun data using Kraken2. So I built only protist database using refseq genomes from NCBI. I used different confidence levels (0 to 0.7) and increased --minimum-…
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BLAST often fails, and also using too many BLAST resources can get you banned from using BLAST. Right now the pipeline fails (in query mode) if it receives no BLAST input. It would be helpful to be a…
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### Publication and Data Information
There are a number of avocado transcriptomes:
- https://www.sciencedirect.com/science/article/pii/S0304423818307064 - Accession: PRJNA258225
PRJNA258225 https…
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toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/2.10.1+galaxy2
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Basically, the problem is that `biodeps-extended` module collides with `biodeps`
(these modules cannot be loaded concurrently, since they differ only by versionsuffix).
Example: TopHat
Also, existin…
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Hello, I am trying to create a model of Macaca Mulatta (mmul) using MetaDraft. I have the `.faa` file for mmul, along with a Homo Sapien `.gbff` file and an SBML file (Recon3D from the BiGG database).…
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Issue to track the list of software to benchmark
- [Blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
- [Bonsai](https://github.com/dnbaker/bonsai)
-…
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Hello,
I'm trying to run PGAP on an HPC cluster using singularity + slurm and I'm running into some troubles.
While pgap is installing/running fine with our "test genome" on the main machine t…
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Can I use this tool with blast database (download from ftp://ftp.ncbi.nih.gov/blast/db/)?
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BLAST+ version>=2.8.1 "supports the new BLAST database version (BLASTDBv5). This is a taxonomically aware version of the BLAST database. See notes at https://ftp.ncbi.nlm.nih.gov/blast/db/v5/blastdbv5…