perEditor

A tool to create personalized genome sequences
 

Home Download  Installation  Usage  VCF format  Tutorial
 

Overview

Usually genomic reads, such as DNA-seq, RNA-seq, or ChIP-seq, are aligned against a unique reference genome. However, mutation and recombination processes produce variations from the reference sequence that can mislead the alignment process. To overcome this problem, is necessary a reference genome that has been modified to contain the variations of the individual from which the samples were taken. Here, we created perEditor, a reference genome editor that creates a copy of the reference sequences that has been modified to reflex information about SNPs and indels. Moreover, a second tool, perEditor_ra, was created to be used on the previously personalized reference sequences to take into account information about chromosome rearrangements. Both perEditor and perEditor_ra are command line tools that runs under Linux systems.
 

perEditor takes as input a fasta file for each one of the chromosomes of the reference genome, and a VCF file that contains information about SNPs and indels of such chromosome. Then, the tool creates a new fasta sequence that is a copy the original sequence, but that has been customized to contain the information contained on the VCF file.  On the other hand, perEditor_ra can be used to further personalized the reference sequences. This time, chromosomal rearrangement information (provided in a VCF file) are used by perEditor_ra to  manage the genetic variations described in the following figure.

Updates

Contact

Marcelo Rivas-Astroza ( rivasas2 AT Illinois DOT edu )