Building the Cornetto C programme requires a compiler that supports C99 standard (with X/Open 7 POSIX 2008 extensions), which is widely available. To build:
sudo apt-get install zlib1g-dev #install zlib development libraries
git clone https://github.com/hasindu2008/cornetto
cd cornetto
make
The commands to zlib development libraries on some popular distributions :
On Debian/Ubuntu : sudo apt-get install zlib1g-dev
On Fedora/CentOS : sudo dnf/yum install zlib-devel
On OS X : brew install zlib
To get the telomere statistics of your assembly (vertebrates with TTAGGG telomere sequence) use the script scripts/telostats.sh. This script uses cornetto subcommands that implements functionality of telomere analysis scripts from the VGP project. If your assembly is asm.fasta:
scripts/telostats.sh asm.fasta
Output:
asm.windows.0.4.50kb.ends.bed: telomeres at the ends of contigsstdout: counts of number of contigs with 1 telomere at the end, 2 telomeres at the end, more than 2 telomeres at the endExample: If you run this on the HG002 Q100 genome, you should see 46 contigs with 2 telomeres at the end.
scripts/telostats.sh hg002v1.0.1.fasta
$ contigs with 2 telo: 46
To generate a dotplot of the mapping between your assembly and a reference genome, use the scripts/minidotplot.sh. This script requires minimap2, samtools. If your assembly is ref.fasta and the reference is asm.fasta:
scripts/minidotplot.sh ref.fasta asm.fasta
Output:
asm.paf: minimap2 alignmentasm.report.tsv: for each assembly contig: which chromosome in the reference is the best match; if it had to be reverse complemented to match the reference; new nameasm.eps: the dot plot in eps formatExamples:
# dot plot of a hifiasm primary assembly against the chm13 haploid cell-line reference`
awk '/^S/{print ">"$2;print $3}' asm.p_ctg.gfa > asm.fasta
scripts/minidotplot.sh chm13.fa asm.fasta
# dot plot of a hifiasm primary assembly against a "haploid" version of the HG002 Q100 reference
samtools faidx hg002v1.0.1.fasta
grep "PATERNAL\|chrEBV\|chrM\|chrX\|chrY" hg002v1.0.1.fasta.gz.fai | cut -f 1 > paternal.txt
samtools faidx hg002v1.0.1.fasta.gz -r paternal.txt -o hg002v1.0.1_pat.fasta
scripts/minidotplot.sh hg002v1.0.1_pat.fasta asm.fasta
# dot plot of hifiasm hap1+hap2 against HG002 Q100 diploid reference
awk '/^S/{print ">"$2;print $3}' asm.hap1.p_ctg.gfa > asm.hap1.fasta
awk '/^S/{print ">"$2;print $3}' asm.hap2.p_ctg.gfa > asm.hap2.fasta
cat asm.hap1.fasta asm.hap2.fasta > asm.hap1+hap2.fasta
scripts/minidotplot.sh hg002v1.0.1.fasta asm.hap1+hap2.fasta
# dot plot of a hifiasm hap1 against the chm13 haploid cell-line reference
scripts/minidotplot.sh hg002v1.0.1.fasta asm.hap1.fasta
To get per-chromosome statistics use the script scripts/asmstats.sh. Make sure you have already run scripts/telostats.sh and scripts/minidotplot.sh before running this script. This is because the files generated in those steps are reused by this script.
scripts/asmstats.sh asm.fasta
Output which is printed to the stdout is explained here.
Examples:
# for a primary assembly called asm.fasta against chm13.fa
scripts/telostats.sh asm.fasta
scripts/minidotplot.sh chm13.fa asm.fasta
scripts/asmstats.sh asm.fasta
# for a primary assembly called asm.fasta against a haploid hg002 we created before
scripts/telostats.sh asm.fasta
scripts/minidotplot.sh hg002v1.0.1_pat.fasta asm.fasta
scripts/asmstats.sh asm.fasta
# for a diploid assembly called asm.hap1+hap2.fasta against hg002v1.0.1.fasta diploid reference
scripts/telostats.sh asm.hap1+hap2.fasta
scripts/minidotplot.sh hg002v1.0.1.fasta asm.hap1+hap2.fasta
scripts/asmstats.sh asm.hap1+hap2.fasta
# for haplotype 1 assembly called asm.hap1.fasta against the chm13
scripts/telostats.sh asm.hap1.fasta
scripts/minidotplot.sh chm13.fa asm.hap1.fasta
scripts/asmstats.sh asm.hap1.fasta
What the aforementioned scripts perform, can also be done manually through individual commands.
minimap2 --eqx -cx asm5 ref.fasta asm.fasta > asm.paf
ref.fasta and asm.fasta are what we detailed under the minidotplot.sh section above. You may want to change the pre-set to asm10 and tune other minimap2 options.
cornetto fixasm asm.fasta asm.paf -r asm.report.tsv -w asm.fix.paf > asm.fix.fasta
Here, the inputs are asm.fasta and asm.paf. asm.report.tsv, asm.fix.paf and asm.fix.fasta are outputs:
asm.fix.paf will contain the asm.paf with +/- directions fixed to match those in the reference.asm.fix.fasta will contain the contigs in asm.fasta but with the directions corrected to match the reference. The contigs are also renamed here based on the chromosome for which the majority of a contig mapped to.asm.report.tsvwill contain a report like the example below that tells for each assembly contig: the chromosome which the majority of the contig mapped; if the direction was swapped; and, the new name for the contig we assigned.
ptg000001l chr3 + chr3_0
ptg000002l chr13 + chr13_0
ptg000003l chr15 + chr15_0
ptg000004l chr5 - chr5_0
cornetto minidot asm.fix.paf -f 2 > asm.eps
You may convert the eps file to pdf to view.
cornetto asmstats asm.paf asm.windows.0.4.50kb.ends.bed -r asm.report.tsv
Here, asm.paf and asm.report.tsv is what we generated in the section “Generate a dot plot step by step” above. ` asm.windows.0.4.50kb.ends.bed is an output from scripts/telostats.sh`.
Output which is printed to the stdout is explained here.
Our Cornetto C programme contains a number of subtools in addition to the ones explained above. For more details of each and every command, see the manual page.