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Analysis of simulated validation data by the CARD team (unpublished) revealed that Prodigal undercalls ORFs when the _-split_prodigal_jobs_ option is used. This was particularly noticeable in a _Acine…
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Hello,
I am trying to use metaphor with my data. I installed it in a cluster (NAME="CentOS Linux", VERSION="8", PLATFORM_ID="platform:el8") using conda. I used DFAST with the default configuration, a…
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Hi, I'm trying the viralFlye pipeline for the first time today, starting with the directory from metaFlye output and the reads. My input command is the following:
~/tools/viralFlye/viralFlye.py --d…
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Anacaonda3
Python 3.7
Windows 10
In the process of installing deepBGC get an error message that the package can't be installed because hmmer and Prodigal are not accessible. Any clarificatio…
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I am currently trying to run MTase linker in v0.4.11. The snakemake commands are failing because spaces are introduced through the workflow. These spaces make all jobs fail.
Command ran:
```
nan…
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Hi, as Prodigal v2.6.3, we observe with pyrodigal a difference in translation result for some start codon (TTG).
>nuc sequence (Lactobacillus)
TTGGGCATACCGGCTGAATACGTCTTATTCGACAGCTGTTTCTCTTCACCTAA…
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A small project to improve anvi'o, based upon feedback/ideas @FlorianTrigodet and I heard from our colleagues at the QIB in Norwich.
## The need
There is interest in being able to use alternativ…
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Can I use _Prodigal_ to **predict fungal genes**?
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Prodigal penalizes predicting genes that are shorter than 250 bp (83 aa). As a result, Prokka is missing a number of short proteins that do exist in a closely related species. Any thoughts on how to d…
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- Prodigal is pretty fast, however, gene `annotation` is missing. Only `gene-calling` done