Telescoper: de novo assembly of highly repetitive regions

Abstract

Motivation: With advances in sequencing technology, it has become faster and cheaper to obtain short-read data from which to assemble genomes. Although there has been considerable progress in the field of genome assembly, producing high-quality de novo assemblies from short-reads remains challenging, primarily because of the complex repeat structures found in the genomes of most higher organisms. The telomeric regions of many genomes are particularly difficult to assemble, though much could be gained from the study of these regions, as their evolution has not been fully characterized and they have been linked to aging.Results: In this article, we tackle the problem of assembling highly repetitive regions by developing a novel algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. Our algorithm, Telescoper, uses short- and long-insert libraries in an integrated way throughout the assembly process. Results on real and simulated data demonstrate that our approach can effectively resolve much of the complex repeat structures found in the telomeres of yeast genomes, especially when longer long-insert libraries are used.Availability: Telescoper is publicly available for download at sourceforge.net/p/telescoper.Contact: yss@eecs.berkeley.eduSupplementary Information: Supplementary data are available at Bioinformatics online.

De novo assembly methods for next generation sequencing data

“…The Telescoper [71] is an SE de novo genome assembler that mainly focuses on highly repetitive regions. It performs the assembly by iteratively extending paths and selecting between them using an empirical distribution, which is computed using long-insert and short-insert PE reads.…”

“…The set of left-mates associated with reads in unitig U is denoted by M U . Telescoper [71] proposes a model to calculate a final score P ext for each possible extension. First, it calculates f U .x/, the expected number of left-reads in M U spanning the position x using the following formula:…”

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

“…Recently developed assemblers SPAdes and Telescoper emphasized a new approach to aggregating read-pair information Pham et al, 2013;Vyahhi et al, 2012;Bresler et al, 2012). In order to resolve the repeats, one needs to estimate the (set of) genomic distances between any two edges in the de Bruijn graph.…”

“…In order to resolve the repeats, one needs to estimate the (set of) genomic distances between any two edges in the de Bruijn graph. Key features of SPAdes and Telescoper (Bresler et al, 2012) include algorithms to approximate these distances by aggregating distance estimates obtained from individual read pairs. Below we complement the heuristics for estimating distances between the edges in the de Bruijn graph described in Bankevich et al (2012); Pham et al (2013); Vyahhi et al (2012);and Bresler et al (2012) by a rigorous likelihood model.…”

Candidate egg case silk genes for the spider Argiope argentata from differential gene expression analyses

“…The polymeric organization of spidroins and lack of complete gene data are problems for differential gene expression analyses that use de novo transcriptomes (transcriptomes assembled without a reference genome). Obtaining complete contigs of long and repetitive transcripts in de novo assemblies is especially difficult (eg Treangen & Salzberg, 2011;Bresler et al, 2012). Although the 5 0 and 3 0 regions of spidroins are nonrepetitive and can be accurately assembled from short RNA-sequencing (RNAseq) reads, assembly of the bulk of RNAseq reads from spidroin genes results in contigs that are incomplete representations of the repetitive region (Clarke et al, 2014.…”