Nature research paper: Recombination between heterologous human acrocentric chromosomes
. This renders sequences and chains of small variants as linear structures, while repeats caused by segmental duplications, inversions and other structural variants tend to form loops.We untangled the pangenome graph by applying ODGI UNTANGLE . Practically, we projected the graph into an alignment between a set of query and reference sequences. We set the following parameter:We segmented the graph into regular-sized regions of ~50 kb , merging regions shorter than 1 kb .
For each query segment, if there were multiple best hits against different targets , we put as the first one the hit having as target the chromosome of origin of the query . We repeated the graph untangling another five times, but constrained the algorithm to use only one of the acrocentric chromosomes of T2T-CHM13 as a target at a time and return the best-matching hit .odgi untangle -i graph.og -e 50000 -m 1000 -n 1 -j 0 -r chr14 -c cuts.txtodgi untangle -i graph.og -e 50000 -m 1000 -n 1 -j 0 -r chr21 -c cuts.txtWe used the cut points generated when using all of the acrocentric chromosomes of T2T-CHM13 as targets .
Finally, we ‘grounded’ the untangled output generated with all acrocentric chromosomes as targets: in more detail, each untangled query segment was placed against a particular acrocentric chromosome by using the untangled outputs constrained to a single target. We split the result by acrocentric chromosome and kept only queries untangling both p- and q-arms of the targets. Furthermore, we removed query segments overlapping regions flagged in the assemblies as unreliable by FLAGGER.
We displayed the aggregated results for each acrocentric chromosome. We used genome annotations for the first 25 Mb of each acrocentric chromosome, using T2T-CHM13v2.0 UCSC trackhub (
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