cornetto

Cornetto

Cornetto is a method for iterative genome assembly using nanopore sequencing from Oxford Nanopore Technologies (ONT). This repository documents the Cornetto bioinformatics protocol and the Cornetto toolkit (a programme written in C and a collection of shell scripts). Cornetto toolkit also features some useful commands for evaluating assemblies generated from any other method.

Documentation: https://hasindu2008.github.io/cornetto

Publication and data

• Preprint link (bioxiv)
• Talk video link (London Calling 2025)
• Datasets used in the preprint

Cornetto bioinformatics protocol

Detailed documentation

See here.

Summary

1. Generate a base assembly. Sequence on a single flowcell as normal and use hifiasm to assemble.
2. Generate a cornetto panel for adaptive sampling. Identify the ‘boringbits’ from the assembly and create a adaptive sampling target panel for rejecting reads.
3. Run adaptive sampling using readfish with the panel created in step 2 for around 24 hours.
4. Create the next iteration of assembly. Use collective data from step 1 and step 3 to create an assembly with hifiasm.
5. Repeat from step 2.

Cornetto toolkit

Detailed documentation

See here.

Summary

Using helper scripts:

scripts/telostats.sh asm.fasta # prints the telomere counts
scripts/minidotplot.sh ref.fasta asm.fasta # creates reference vs assembly dotplot in assembly.eps
scripts/asmstats.sh asm.fasta  # prints chromosome-wise assembly to reference report

Using individual commands:

# creating a dot plot
## 1. align assembly to reference
minimap2 -t16 --eqx -cx asm5 ref.fasta asm.fasta > asm.paf
## 2. fix the +/- directions to match the reference
cornetto fixasm asm.fasta asm.paf -r asm.report.tsv -w asm.fix.paf > asm.fix.fasta
## 3. dot plot
cornetto minidot asm.fix.paf -f 2 > asm.eps

# per-chromosome evaluation
cornetto asmstats asm.paf asm.windows.0.4.50kb.ends.bed -r asm.report.tsv -s ref.fasta
# asm.windows.0.4.50kb.ends.bed is from `scripts/telostats.sh`

# miscellaneous commands
cornetto fa2bed asm.fasta > asm.bed  # create a bed file with assembly contig lengths
cornetto seq -m 10000 reads.fastq > long.fastq # extract reads >=10kb

Acknowledgement

• cornetto uses klib (MIT licensed).
• cornetto minidot is simply minidot from miniasm (MIT licensed).
• cornetto sdust is simply sdust.
• cornetto telofind, telobreaks & telowin are implemented based on VGP telomere scripts (BSD licensed).

This site is open source. Improve this page.