An integer linear programming approach for genome scaffolding

This paper presents a simple and fast approach for genome scaffolding, combining constraint modeling and simple graph manipulation. We model the scaffolding problem as an optimization problem on a graph built from a paired-end reads alignment on contigs, then describe an heuristic to solve this problem with the iterative combination of local constraints solving and cycle breaking phases. We tested our approach on a benchmark of various genomes, and compared it with several usual scaffolders. The proposed method is quick, flexible, and provides results comparable to other scaffolders in terms of quality. In addition, contrarily to state of the art approaches that require dedicated servers, it can be run on a basic notebook computer even for large genomes.

[1]  Eugene W. Myers,et al.  The greedy path-merging algorithm for contig scaffolding , 2002, JACM.

[2]  Zhanjiang Liu.  DNA Sequencing Technologies , 2007 .

[3]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[4]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[5]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[6]  Daniel Le Berre,et al.  The Sat4j library, release 2.2 , 2010, J. Satisf. Boolean Model. Comput..

[7]  Adel Dayarian,et al.  SOPRA: Scaffolding algorithm for paired reads via statistical optimization , 2010, BMC Bioinformatics.

[8]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[9]  Wing-Kin Sung,et al.  Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences , 2011, RECOMB.

[10]  Esko Ukkonen,et al.  Fast scaffolding with small independent mixed integer programs , 2011, Bioinform..

[11]  Walter Pirovano,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

[12]  M. Schatz,et al.  Algorithms Gage: a Critical Evaluation of Genome Assemblies and Assembly Material Supplemental , 2008 .

[13]  Marcel J. T. Reinders,et al.  GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies , 2012, Bioinform..

[14]  Rayan Chikhi,et al.  Space-efficient and exact de Bruijn graph representation based on a Bloom filter , 2012, Algorithms for Molecular Biology.

[15]  Albert Oliveras,et al.  A New Look at BDDs for Pseudo-Boolean Constraints , 2012, J. Artif. Intell. Res..

[16]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[17]  M. Berriman,et al.  A comprehensive evaluation of assembly scaffolding tools , 2014, Genome Biology.

[18]  Albert Oliveras,et al.  A Parametric Approach for Smaller and Better Encodings of Cardinality Constraints , 2013, CP.

[19]  Nilgun Donmez,et al.  SCARPA: scaffolding reads with practical algorithms , 2013, Bioinform..

[20]  Annie Chateau,et al.  Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem , 2014, AlCoB.