What it does

This tool merges two FASTA or FASTQ files into a single FASTA file using IUPAC ambiguity codes where appropriate. When differences occur between the sequences, ambiguity codes are used to represent possible variations.

Example:

>seq1
ACTGACTGAAA

>seq2
ACTGAMTGCGN

will result in:

>seq1
ACTGAMTGMRN

If the -m option is in use, however, the tool will pick the least ambiguous base if there is no contradiction between the symbols in the inputs. Conflicts are indicated by using x in the merged sequence and the picked base is converted to lowercase if the less specific symbol is an N to express uncertainty. With this logic the input sequences above will result in the merge result:

>seq1
ACTGACTGxxa

Attribution

This Galaxy tool relies on the seqtk toolkit from lh3/seqtk, developed by Heng Li at the Broad Institute