position of overlaps in final assembly

[mariellev]

Is it possible to find out where the positions of the joints/overlaps are in the contigs of an hifiasm assembly ?

[chhylp123]

Which types of overlap do you need?

[mariellev]

We have found some small stretch of contaminant sequences in our assembly - we would like to check that the joint wasn't made by overlapping the sequences of the contaminants.

[chhylp123]

In GFA files, hifiasm outputs the read IDs and their coordinates if they are used in building assemblies (see A-lines at: https://hifiasm.readthedocs.io/en/latest/interpreting-output.html#interpreting-output).