Mafft - Align Sequences In ReferenceΒΆ

Align sequences (globally) in the reference fasta file to identify homology regions

Location

  • Filepath: <SnakeLines_dir>/rules/shared/reference/alignment/mafft.snake
  • Rule name: mafft__align_sequences_in_reference

Input(s):

  • reference: Reference sequences in FASTA format

Output(s):

  • alignment: Aligned sequences in ALN format

Param(s):

  • genbank_ids: List of Genbank identifiers for sequences to download
  • email: Inform NCBI who you are to contact you in case of excessive use. Otherwise they may block your access directly.