Tools : tl

Run execute scripts

Graph Alignment

tl.graphIdx	Index the graph for graph alignment.
tl.graphAlign	Align ONT reads to the graph.

QV check

tl.mkMeryl	Create meryl database for k-mer counting.
tl.calQV	Perform quality evaluation using Merqury's qv.sh script.

Chromosome assignment and Contig QC

tl.getT2T	Run the script to calculate assembly statistics, including contig presence, telomere regions, and gap locations.
tl.rmrDNA	Generate a GFA file with rDNA sequences removed from the graph.
tl.chrAssign	Run the script to align the assembly to the given reference using mashmap and obtain the chromosome assignment results.
tl.showPairwiseAlign	Generate a dot plot from the mashmap output.
tl.mapBetweenNodes	Map the query sequences to the reference sequences using mashmap.

Insert gaps

tl.insertGap

Find ONT support for Inserts a gap into the graph using split reads.

Modifying assembly

tl.sortContig	Sorts sequences in a FASTA file based on a custom sorting criterion (e.g., 'hap', 'chr').
tl.renameContig	Rename the contigs in the FASTA file based on the provided chromosome map file.
tl.detect_internal_telomere	Detect internal telomere in the assembly.fasta file.
tl.runTrimming	Trim the contigs based on the provided coordinates.
tl.flipContig	Flip the sequences in a FASTA file based on the provided list of contigs.
tl.convertRefName	Replace the name in the given FASTA file.
tl.filterContigs	Filter the contigs in the FASTA file based on the provided list of contigs.