These tracks show the one-to-one v1_nfLO alignments of the GRCh38/hg38 to the
T2T-CHM13 v2.0 assembly.
The track displays boxes joined together by either single or double lines,
with the boxes represent aligning regions, single lines indicating gaps that
are largely due to a deletion in the CHM13 v2.0 assembly or an insertion in
the GRCh38/hg38, and double lines representing more complex gaps that involve
substantial sequence in both assembly.
To prevent ambiguous alignments, all false duplications, as determined by the Genome in a Bottle Consortium
as well as the GRCh38 modeled centromeres,
were masked from the GRCh38/hg38 primary assembly. In addition, unlocalized and unplaced (random) contigs were removed.
Alignment and Chain Creation
For the minimap2-based pipeline, the initial chain file was generated using
nf-LO v1.5.1 with
minimap2 v2.24 alignments. These
chains were then split at all locations that contained unaligned segments greater than 1kbp or
gaps greater than 10kbp. Split chain files were then converted to PAF format
with extended CIGAR strings using chaintools (v0.1),
and alignments between nonhomologous chromosomes were removed. The trim-paf operation of
was next used to remove overlapping alignments
in the query sequence, and then the target sequence, to create 1:1 alignments. PAF alignments
were converted back to the chain format with paf2chain commit f68eeca, and finally,
chaintools was used to generate the inverted chain file.
Full commands with parameters used were:
nextflow run main.nf --source GRCh38.fa --target chm13v2.0.fasta --outdir dir -profile local --aligner minimap2
python chaintools/src/split.py -c input.chain -o input-split.chain
python chaintools/src/to_paf.py -c input-split.chain -t target.fa -q query.fa -o input-split.paf
awk '$1==$6' input-split.paf | rb break-paf --max-size 10000 | rb trim-paf -r | rb invert | rb trim-paf -r | rb invert > out.paf
paf2chain -i out.paf > out.chain
python chaintools/src/invert.py -c out.chain -o out_inverted.chain
The above process does not add chain ids or scores. The UCSC utilities
chainScore are used to update the
chainMergeSort out.chain | chainScore stdin chm13v2.0.2bit hg38.2bit chm13v2.0-hg38.chain
chainMergeSort out_inverted.chain | chainScore stdin hg38.2bit chm13v2.0.2bit hg38-chm13v2.0.chain
uses dynamic programming and the CIGAR string to find an optimal
splitting point between overlapping alignments in the query sequence. It
starts its trimming with the largest overlap and then recursively trims
Results were validated by using chaintools to confirm that there were no
overlapping sequences with respect to both CHM13v2.0 and GRCh38 in the
released chain file. In addition, trimmed alignments were visually inspected
with SafFire to confirm their quality.
Chains were swapped to make GRCh38/hg38 the target.
The v1_nflo chains were generated by Nae-Chyun Chen<firstname.lastname@example.org>
and Mitchell Vollger<email@example.com>
Nurk S, Koren S, Rhie A, Rautiainen M, et al. The complete sequence of a human genome. bioRxiv, 2021.