Notes

• ambiguous bases are excluded during 'collect_homologs'
• sed command in translate function removes frame-info suffix (_1) from ids
• where is the correct step to remove duplicates, beginning and homologs?
• write script to regenerate duplicates
  • where should duplicates be reintroduced?
• multiple substitutions at the same codon lead to weird behavior, investigate
• How can I make ambiguous not count towards indentity? Should be filtered
• Write script to impute msa for amiguity handling. Fasta -> Transpose -> Transpose -> Fasta
• Remove percent identity 'magic number' in ava_homologs

UpDownSelect

Installation Process

git clone https://github.com/StefanFrankBio/UpDownSelect.git
micromamba env create -f environments/UpDownSelect.yml
micromamba activate UpDownSelect

Input Data

1. fasta file containing nucleotide sequences to be analyzed
2. reference fasta file containing nucleotide sequences for genes of interest
3. tsv file containing metadata

How to run the pipeline

UpDownSelect sequences.fasta references.fasta metadata.tsv output_directory threads

Workflow

Step1: Extract Orfs