I often use 'bwa mem' to align a set of contigs to a reference genome. 'bwa' is able to read its input either from FASTQ or from FASTA files. Thus you can simply feed a set of contigs into 'bwa' instead of a set of sequencing reads:

bwa mem reference.fasta contigs.fasta > output.sam

If your contigs are spread over several files, you can pipe them into 'bwa' (the trailing '-' causes 'bwa' to read from stdin):

cat contig*.fasta | bwa mem reference.fasta - > output.sam

Note, that 'bwa mem' does a local alignment, it only aligns the best matching parts of your contigs while the remainder is clipped off. Technically, it is also possible to put several reference genomes into 'reference.fasta', thus aligning the contigs to several reference genomes in one run. But since it is a local alignment, the result will most likely be very confusing.

Hi again. I have used QUAST to analyze my contigs against a reference, and one of the results is an image (svg) of the alignment of my contigs and the reference. Does anyone knows if I can retrieve such alignment in a fasta format? Thanks a lot.

Thanks, I've been trying your suggestions, with no success.

Does anyone knows if MITObim can be used with contigs? (align contigs to a reference genome), or only reads in fastq can be used?

Thanks