<![CDATA[BOL: Alignment of closely related whole genomes/scaffolds]]> https://bioinformaticsonline.com/bookmarks/view/26179/alignment-of-closely-related-whole-genomesscaffolds? https://bioinformaticsonline.com/bookmarks/view/26179/alignment-of-closely-related-whole-genomesscaffolds Fri, 29 Jan 2016 10:37:27 -0600 https://bioinformaticsonline.com/bookmarks/view/26179/alignment-of-closely-related-whole-genomesscaffolds <![CDATA[Alignment of closely related whole genomes/scaffolds]]> 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.

Address of the bookmark: http://www.cs.utoronto.ca/~brudno/721.full.pdf

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/26179/alignment-of-closely-related-whole-genomesscaffolds#item-annotation-2315 Fri, 29 Jan 2016 10:46:17 -0600 https://bioinformaticsonline.com/bookmarks/view/26179/alignment-of-closely-related-whole-genomesscaffolds#item-annotation-2315 <![CDATA[Comment by Jitendra Narayan]]> 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.

]]> Jitendra Narayan