Hi, I have two multifasta files. I want to merge them deleting all those fasta seqences from the first multifasta file which are also in the second file. I need to do it by header comparison, sequences are different under the same headers.

Alternatively, could somebody give me a hint how to generate all the contigs (even those unchanged) through bcftools consensus?

Thanks,
Pawel
You can use the BBMap package like this:

    filterbyname.sh in=file1.fasta names=file2.fasta exclude out=file1_filtered.fasta
    cat file1_filtered.fasta file2.fasta > combined.fasta

