I have an 800 kbp consensus scaffold fastq with many runs of Ns (by design). This was built by mapping reads against a reference and calculating the consensus as a single fastq sequence. Now I want to align the scaffold to the original reference, which should be easy since they are the same lengths and have the same starting positions. The end goal is a .sam of the scaffold aligned to the reference, but keeping the scaffold intact without any clipping/trimming, and preserving IUPAC ambiguities.
So far I’ve tried: Minimap2 and bwa — both align one part of the consensus (flag 0 from Minimap2 .sam) and soft-clip the remainder, and then create many supplementary alignments (flag 2048) from dozens of other fragments pulled from the consensus. Bowtie2 — won’t start because it thinks there are more read characters than quality values (there aren’t, I checked the lengths).
Can I force Minimap2 or bwa to align the whole scaffold without clipping? Or is there another program that would make quick work of this? Seems so simple but is giving me a headache.
Sincere thanks.
From your description of the problem, I think Mauve or MUMmer would do what you want. Do you need sam output?