9. Realign allele sequences

align_contigs.py

####Run the script In this step we use the same alignment script, which we used to align the contigs in step 6. The only difference this time is that we add the --ambiguous flag, indicating that some of our sequences may contain ambiguous characters (such as N's). All sequences we want to align are stored in one fasta file which is named joined_allele_sequences_all_samples.fasta and can be found in the output folder of the previous phasing step (step 8).

#####Example python2.7 align_contigs.py --sequence path/to/phasing-results/joined_allele_sequences_all_samples.fasta --output path/to/alignment-folder/phased --ambiguous