Mapping short sequencing reads to distant relatives

Authors:
Vinicio Reynoso;Catherine Putonti
Affiliations:
Loyola University Chicago, Chicago, IL;Loyola University Chicago, Chicago, IL
Venue:
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Year:
2011

Citing 9
Cited 0

ZOOM! Zillions of oligos mapped

Bioinformatics
MOM

Bioinformatics
CloudBurst

Bioinformatics
SOAP2

Bioinformatics
PerM

Bioinformatics
Updates to the RMAP short-read mapping software

Bioinformatics
Fast and accurate long-read alignment with Burrows–Wheeler transform

Bioinformatics
X-MATE

Bioinformatics
SHRiMP2

Bioinformatics

Quantified Score

Hi-index	0.00

Visualization

Abstract

Numerous different algorithmic approaches have been developed to map the short-reads produced by next-generation sequencing technologies onto reference genome sequences. When sufficiently close reference genomes do not exist, less rigorous approaches must be taken, as is the case for analysis of diverse environmental samples. We have developed a new suite of data structures and algorithms specifically for the mapping of reads from environmental sequencing projects. A pipeline was developed which can rigorously map reads to genomes with many mismatches between the two. Using 50+ million reads generated from soil samples, we present the results of our performance analysis of our approach.