Modern technologies and algorithms for scaffolding assembled genomes

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

(2018) Bai-Han Zhu et al.   BMC GENOMICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

(2018) Michael Schmid et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

(2018) Jisen Zhang et al.   NATURE GENETICS

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data

(2017) Wen-Biao Jiao et al.   GENOME RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

HINGE: long-read assembly achieves optimal repeat resolution

(2017) Govinda M. Kamath et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

(2017) Chuan-Le Xiao et al.   NATURE METHODS

Gramene 2018: unifying comparative genomics and pathway resources for plant research

(2017) Marcela K Tello-Ruiz et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Improvements in Genomic Technologies: Application to Crop Genomics

(2017) Yuxuan Yuan et al.   TRENDS IN BIOTECHNOLOGY

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

(2017) Minh Duc Cao et al.   Nature Communications

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

The combination of direct and paired link graphs can boost repetitive genome assembly

(2016) Wenyu Shi et al.   NUCLEIC ACIDS RESEARCH

Rascaf: Improving Genome Assembly with RNA Sequencing Data

(2016) Li Song et al.   Plant Genome

AGOUTI: improving genome assembly and annotation using transcriptome data

(2016) Simo V. Zhang et al.   GigaScience

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

The Theory and Practice of Genome Sequence Assembly

(2015) Jared T. Simpson et al.   Annual Review of Genomics and Human Genetics

MeDuSa: a multi-draft based scaffolder

(2015) Emanuele Bosi et al.   BIOINFORMATICS

Maligner: a fast ordered restriction map aligner

(2015) Lee M. Mendelowitz et al.   BIOINFORMATICS

Sealer: a scalable gap-closing application for finishing draft genomes

(2015) Daniel Paulino et al.   BMC BIOINFORMATICS

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution

(2015) S. Kasar et al.   Nature Communications

NxRepair: error correction inde novosequence assembly using Nextera mate pairs

(2015) Rebecca R. Murphy et al.   PeerJ

Computational methods for optical mapping

(2015) Lee Mendelowitz et al.   GigaScience

ExSPAnder: a universal repeat resolver for DNA fragment assembly

(2014) A. D. Prjibelski et al.   BIOINFORMATICS

Ragout--a reference-assisted assembly tool for bacterial genomes

(2014) M. Kolmogorov et al.   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

CAR: contig assembly of prokaryotic draft genomes using rearrangements

(2014) Chin Lung Lu et al.   BMC BIOINFORMATICS

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

(2014) Andrew Adey et al.   GENOME RESEARCH

High-quality genome (re)assembly using chromosomal contact data

(2014) Hervé Marie-Nelly et al.   Nature Communications

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

High-throughput genome scaffolding from in vivo DNA interaction frequency

(2013) Noam Kaplan et al.   NATURE BIOTECHNOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

SCARPA: scaffolding reads with practical algorithms

(2012) N. Donmez et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Fast scaffolding with small independent mixed integer programs

(2011) L. Salmela et al.   BIOINFORMATICS

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

(2011) Joshua Wetzel et al.   BMC BIOINFORMATICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Scaffold filling, contig fusion and comparative gene order inference

(2010) Adriana Munoz et al.   BMC BIOINFORMATICS

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

(2010) Adel Dayarian et al.   BMC BIOINFORMATICS

Scaffolding a Caenorhabditis nematode genome with RNA-seq

(2010) A. Mortazavi et al.   GENOME RESEARCH

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reordering contigs of draft genomes using the Mauve Aligner

(2009) Anna I. Rissman et al.   BIOINFORMATICS

r2cat: synteny plots and comparative assembly

(2009) P. Husemann et al.   BIOINFORMATICS

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Breakpoint graphs and ancestral genome reconstructions

(2009) M. A. Alekseyev et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

(2009) Daniel R. Zerbino et al.   PLoS One

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Scaffolding and validation of bacterial genome assemblies using optical restriction maps

(2008) N. Nagarajan et al.   BIOINFORMATICS

Discovering multi–level structures in bio-molecular data through the Bernstein inequality

(2008) Alberto Bertoni et al.   BMC BIOINFORMATICS