De novo fragment assembly with short mate-paired reads: Does the read length matter?

By Mark J. P. Chaisson, Dumitru Brinza, Pavel A. Pevzner. Genome Research, 2009

298 citations recorded by the source corpus.

Increasing read length is currently viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of length, GapLength) opens a possibility to transform short mate-pairs into long mate-reads of length approximately GapLength, and thus raises the question as to whether the read length (as opposed to GapLength) even matters. We describe a new tool, EULER-USR, for assembling mate-paired short reads and use it to analyze the question of whether the read length matters. We further complement the ongoing experimental efforts to maximize read length by a new computational approach for increasing the effective read length. While the common practice is to trim the error-prone tails of the reads, we present an approach that substitutes trimming with error correction using repeat graphs. An important and counterintuitive implication of this result is that one may extend sequencing reactions that degrade with length "past their prime" to where the error rate grows above what is normally acceptable for fragment assembly.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2ffdd6ef0f6f8e96a1cb31d1050797a0bf01f112

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In Molecular Biology

Citations in the corpus

Genome structural variation discovery and genotyping (2011, unknown): “Well-known de novo assembly algorithms for next-generation whole-genome shotgun (NG-WGS) data include EULER-US”
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing (2012, background): “While many heuristics for analysis of read-pairs (called bireads(2) below) have been proposed (Pevzner et al., 2001; Pevzner and Tang, 2001; Zerbino and Birney, 2008; Butler et al., 2008; Simpson et al., 2009; Chaisson et al., 2009; Li et al., 2010), proper utilization of bireads remains, arguably, ”
Biofuels from algae: challenges and potential (2010, methodology): “Fortunately, highthroughput sequencing strategies can be adapted to generate transcriptome data, either by aligning cDNA sequence data to an assembled genome or through de novo transcriptome assembly [111,112].”
Limitations of next-generation genome sequence assembly (2010, methodology): “As argued by groups that presented various implementations of this approach (for example, the algorithms named EULER-US”
The impact of next-generation sequencing on genomics (2011, background): “The primary goal of current algorithms and computing for short-read assembly with NGS technologies is to increase read length (Chaisson et al., 2009).”
Assembly Algorithms for Next-Generation Sequencing Data (2010, unknown): “It was subsequently modified for short 454 GS20 reads [53], even shorter unpaired Illumina/Solexa reads [54], and paired-end Solexa reads [55].”
Using the Velvet de novo assembler for short-read sequencing technologies (2010, methodology): “Sequence ﬁles in FASTA ( APPENDIX 1B ), FASTQ (Cock et al., 2010), SAM, or BAM format (Li et al., 2009).”
IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler (2010, background): “shorter length, higher coverage, but relatively higher error rates) when compared to traditional Sanger reads, new assembly tools have emerged [ 2-11 ].”
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth (2012, methodology): “To speed up the process, an error correction step is conducted to correct reads of high-depth regions that can be aligned to highconfident contigs.”
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies (2010, methodology): “2Infectiologie et Immunologie, Centre de Recherche du CHUQ, Québec, Canada.”
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products (2013, unknown): “…show that it improves on A5 (Tritt et al., 2012), ABySS ASSEMBLING SINGLE CELL GENOMES AND MINI-METAGENOMES (Simpson et al., 2009), CLC, 1 EULER-SR (Chaisson et al., 2009), Ray (Boisvert et al., 2010), SOAPde-novo (Li et al., 2010), and Velvet (Zerbino and Birney, 2008) in multicell bacterial…”
Quake: quality-aware detection and correction of sequencing errors (2010, methodology): “De Bruijn graph-based short read assemblers [10,11,13,20,21] perform substantial error correction of reads in the de Bruijn graph.”
Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data (2013, background): “To further improve correcting quality, Chaisson et al. (2004) introduced a dynamic programming approach that corrects errors by minimizing edit distances.”