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Genome-wise reference packages #69

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cmorganl opened this issue Jan 15, 2021 · 0 comments
Open

Genome-wise reference packages #69

cmorganl opened this issue Jan 15, 2021 · 0 comments
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feature request A request for a new feature unlike one that already exists

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@cmorganl
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Reference packages created from a set of genomes.

Inputs:

  1. One or more fasta files containing genome sequences
  2. A profile HMM the user would like to build a reference package for
  3. If a user provided a single fasta file, a table is required to map sequence names to NCBI taxid, lineage, or other (optional)

Steps:

  1. Predict ORFs with Prodigal
  2. Rename ORFs after the taxonomic label of the genomes
  3. Pull homologous sequences identified by the profile HMM
  4. treesapp create
@cmorganl cmorganl added the feature request A request for a new feature unlike one that already exists label Jan 15, 2021
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@cmorganl