GapFiller: a de novo assembly approach to fill the gap within paired reads

Abstract

BackgroundNext Generation Sequencing technologies are able to provide high genome coverages at a relatively low cost. However, due to limited reads' length (from 30 bp up to 200 bp), specific bioinformatics problems have become even more difficult to solve. De novo assembly with short reads, for example, is more complicated at least for two reasons: first, the overall amount of "noisy" data to cope with increased and, second, as the reads' length decreases the number of unsolvable repeats grows. Our work's aim is to go at the root of the problem by providing a pre-processing tool capable to produce (in-silico) longer and highly accurate sequences from a collection of Next Generation Sequencing reads.ResultsIn this paper a seed-and-extend local assembler is presented. The kernel algorithm is a loop that, starting from a read used as seed, keeps extending it using heuristics whose main goal is to produce a collection of error-free and longer sequences. In particular, GapFiller carefully detects reliable overlaps and operates clustering similar reads in order to reconstruct the missing part between the two ends of the same insert. Our tool's output has been validated on 24 experiments using both simulated and real paired reads datasets. The output sequences are declared correct when the seed-mate is found. In the experiments performed, GapFiller was able to extend high percentages of the processed seeds and find their mates, with a false positives rate that turned out to be nearly negligible.ConclusionsGapFiller, starting from a sufficiently high short reads coverage, is able to produce high coverages of accurate longer sequences (from 300 bp up to 3500 bp). The procedure to perform safe extensions, together with the mate-found check, turned out to be a powerful criterion to guarantee contigs' correctness. GapFiller has further potential, as it could be applied in a number of different scenarios, including the post-processing validation of insertions/deletions detection pipelines, pre-processing routines on datasets for de novo assembly pipelines, or in any hierarchical approach designed to assemble, analyse or validate pools of sequences.

Gap Filling as Exact Path Length Problem

“…For example, the method applies to finding a sequence to span the gap between the two ends of paired-end reads (Nadalin et al, 2012). However, the practical instances for this problem tend to be easier, since paired-end reads are randomly sampled from the genome, whereas in gap filling the easy regions of the genome have already been reconstructed by the contig assembler, and thus only the hard regions are left.…”

TheDitylenchus destructorgenome provides new insights into the evolution of plant parasitic nematodes

“…Then, subreads from PacBio were used to improve the assembly in PBJelly (http://sourceforge.net/projects/pb-jelly). The last step of the assembly was to use all of the paired-and mate-end reads to fill the gaps with GapFiller [17].…”

Genomic Analysis of Pure Cultures and Communities

“…Those unknown nucleotide blocks are called gaps and also can be resolved by computational approach by using pairedread information. This method is implemented in GapFiller software also distributed by BaseClear BV [15]. GapFiller uses local assembly, based upon extending contig ends by paired reads, partially mapped to termini of adjacent contigs.…”