Alignment of closely related whole genomes/scaffolds
By Rahul Nayak 3003 days ago Comments (1)
http://www.cs.utoronto.ca/~brudno/721.full.pdf
With the relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life. This increasing volume of data requires tools that can quickly compare multiple whole-genome sequences, millions of base pairs in length, to aid in the study of populations, pan-genomes, and genome evolution.This bookmaks have been created to report new tools for whole genome alignments.
Please report new whole genome alignment tools under comment sections.
Comments
Hmmm great link Rahul, You can also try Mugsy: fast multiple alignment of closely related whole genomes http://bioinformatics.oxfordjournals.org/content/27/3/334
In my works, I have also used BWA-SW, BLAT and LASTZ. However, LASTZ is not well-suited for aligning to many chromosomes at once. Whereas, the BLAT is difficult as PSL to BAM conversion is imperfect in it.