This program is a CLI for chr.Intersect package. The program finds
homologous regions common for a set of closely related input
nucleotide sequences.
Given that you have git, golang, and make:
git clone https://github.com/IvanTsers/intersect
cd intersect
make
Change to tutorial:
cd tutorial
There are 10 sequences containing from 1 to 4 marker regions. We run
intersect using t1.fasta as a reference and sequences in t as
queries:
intersect -r t1.fasta t/*
This will return a perfect intersection, that is, a region shared by
all sequences. It contains only one of the markers. We lower the
sensitivity threshold to 0.9:
intersect -r t1.fasta -f 0.9 t/*
This returns two markers shared by at leat 9 out of 10 genomes. We continue to lower the sensitivity of intersection and add switches to print mutation positions:
intersect -r t1.fasta -f 0.6 -n t/*
This time the second marker includes an additional region separated
with mismatches shown as N. These regions are found in at least 6
out of 10 genomes. We lower the sensitivity threshold again:
intersect -r t1.fasta -f 0.2 -n t/*
The intersection now contains all four markers from the directory
markers.