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References from A deep dive into genome assemblies of non-vertebrate animals. Local targets link to admitted publications; unresolved targets remain external evidence.
New Approaches for Genome Assembly and Scaffolding
10.1146/annurev-animal-020518-115344 · 2019 · External reference
Unresolved reference
2021 · External reference
Unresolved reference
External reference
The Timetree of Life
10.1093/sysbio/syp042 · 2009 · External reference
Animal biodiversity: An update of classification and diversity in 2013”. In: Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013)
10.11646/zootaxa.3703.1.3 · 2013 · External reference
Insect genomes: progress and challenges
10.1111/imb.12599 · 2019 · External reference
Research trends in ecosystem services provided by insects
10.1016/j.baae.2017.09.006 · 2018 · External reference
The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance
10.1186/s12915-016-0321-y · 2016 · External reference
Genome Sequence of Aedes aegypti, a Major Arbovirus Vector
10.1126/science.1138878 · 2007 · External reference
The Genome of Anopheles darlingi , the main neotropical malaria vector
10.1093/nar/gkt484 · 2013 · External reference
Improved reference genome of Aedes aegypti informs arbovirus vector control
10.1038/s41586-018-0692-z · 2018 · External reference
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
10.1126/science.aal3327 · 2017 · External reference
Toward a genome sequence for every animal: Where are we now?
10.1073/pnas.2109019118 · 2021 · External reference
Marine natural products
10.1039/c9np00069k · 2020 · External reference
Marine Natural Products: A Source of Novel Anticancer Drugs
10.3390/md17090491 · 2019 · External reference
Antibacterial products of marine organisms
10.1007/s00253-015-6553-x · 2015 · External reference
Terpenoids in Marine Heterobranch Molluscs
10.3390/md18030162 · 2020 · External reference
Natural Products from Sponges
10.1007/978-94-024-1612-1_15 · 2019 · External reference
Molluscan Genomics: Implications for Biology and Aquaculture
10.1007/s40610-017-0077-3 · 2017 · External reference
Invertebrates, ecosystem services and climate change
10.1111/brv.12002 · 2012 · External reference
Molluscan genomics: the road so far and the way forward
10.1007/s10750-019-04111-1 · 2019 · External reference
The Biology and Evolution of Calcite and Aragonite Mineralization in Octocorallia
10.3389/fevo.2021.623774 · 2021 · External reference
Molecular mechanisms of biomineralization in marine invertebrates
10.1242/jeb.206961 · 2020 · External reference
Using the Acropora digitifera genome to understand coral responses to environmental change
10.1038/nature10249 · 2011 · External reference
The Roles of Introgression and Climate Change in the Rise to Dominance of Acropora Corals
10.1016/j.cub.2018.08.061 · 2018 · External reference
Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching
10.1126/science.aba4674 · 2020 · External reference
Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes
10.1093/molbev/msaa216 · 2020 · External reference
Phylogenetic tree building in the genomic age
10.1038/s41576-020-0233-0 · 2020 · External reference
Genomic insights into the evolutionary origin of Myxozoa within Cnidaria
10.1073/pnas.1511468112 · 2015 · External reference
Comparative genomics and the nature of placozoan species
10.1371/journal.pbio.2005359 · 2018 · External reference
The Mutational Meltdown in Asexual Populations
10.1093/oxfordjournals.jhered.a111354 · 1993 · External reference
The Ecoresponsive Genome of Daphnia pulex
10.1126/science.1197761 · 2011 · External reference
A New Reference Genome Assembly for the Microcrustacean Daphnia pulex
10.1534/g3.116.038638 · 2017 · External reference
Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes
10.1016/j.isci.2019.10.039 · 2019 · External reference
Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova
10.1073/pnas.2101485118 · 2021 · External reference
Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga
10.1126/sciadv.abg4216 · 2021 · External reference
The Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity
10.1111/j.1467-9388.2011.00703.x · 2011 · External reference
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
10.1093/bioinformatics/btv351 · 2015 · External reference
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
10.1093/molbev/msx319 · 2017 · External reference
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes
10.1093/molbev/msab199 · 2021 · External reference
Basic local alignment search tool
10.1016/s0022-2836(05)80360-2 · 1990 · External reference
The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes
10.1093/jhered/est084 · 2013 · External reference
Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)
10.1071/is16059 · 2017 · External reference
Earth BioGenome Project: Sequencing life for the future of life
10.1073/pnas.1720115115 · 2018 · External reference
Unresolved reference
2021 · External reference
Unresolved reference
2021 · External reference
The era of reference genomes in conservation genomics
10.1016/j.tree.2021.11.008 · 2022 · External reference
DNA sequencing with chain-terminating inhibitors
10.1073/pnas.74.12.5463 · 1977 · External reference
Life with 6000 Genes
10.1126/science.274.5287.546 · 1996 · External reference
Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology
10.1126/science.282.5396.2012 · 1998 · External reference
The A, C, G, and T of Genome Assembly
10.1155/2016/6329217 · 2016 · External reference
Initial sequencing and analysis of the human genome
10.1038/35057062 · 2001 · External reference
Bioinformatics challenges of new sequencing technology
10.1016/j.tig.2007.12.006 · 2008 · External reference
Genome sequencing in microfabricated high-density picolitre reactors
10.1038/nature03959 · 2005 · External reference
An integrated semiconductor device enabling non-optical genome sequencing
10.1038/nature10242 · 2011 · External reference
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
10.1101/gr.091868.109 · 2009 · External reference
Sequencing technologies — the next generation
10.1038/nrg2626 · 2009 · External reference
Accurate whole human genome sequencing using reversible terminator chemistry
10.1038/nature07517 · 2008 · External reference
Long reads: their purpose and place
10.1093/hmg/ddy177 · 2018 · External reference
Real-Time DNA Sequencing from Single Polymerase Molecules
10.1126/science.1162986 · 2009 · External reference
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
10.1038/s41587-019-0217-9 · 2019 · External reference
Three decades of nanopore sequencing
10.1038/nbt.3423 · 2016 · External reference
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
10.1186/s13059-016-1103-0 · 2016 · External reference
Performance of neural network basecalling tools for Oxford Nanopore sequencing
10.1186/s13059-019-1727-y · 2019 · External reference
Nanopore sequencing and assembly of a human genome with ultra-long reads
10.1038/nbt.4060 · 2018 · External reference
Unresolved reference
External reference
Unresolved reference
2017 · External reference
Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
10.1101/2021.10.27.466057 · 2021 · External reference
Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform
10.7717/peerj.10340 · 2020 · External reference
High-Throughput Gene Mapping in Caenorhabditis elegans
10.1101/gr.208902 · 2002 · External reference
The Atlas Genome Assembly System
10.1101/gr.2264004 · 2004 · External reference
CAP3: A DNA Sequence Assembly Program
10.1101/gr.9.9.868 · 1999 · External reference
Consensus generation and variant detection by Celera Assembler
10.1093/bioinformatics/btn074 · 2008 · External reference
An Eulerian path approach to DNA fragment assembly
10.1073/pnas.171285098 · 2001 · External reference
Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes
10.1126/science.1072104 · 2002 · External reference
Minimus: a fast, lightweight genome assembler
10.1186/1471-2105-8-64 · 2007 · External reference
Genome sequence assembly using trace signals and additional sequence information
1999 · External reference
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
10.1101/gr.8.3.186 · 1998 · External reference
The Phusion Assembler
10.1101/gr.731003 · 2002 · External reference
Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons
10.1093/bioinformatics/btq646 · 2010 · External reference
TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing Projects
10.1089/gst.1995.1.9 · 1995 · External reference
ABySS: A parallel assembler for short read sequence data
10.1101/gr.089532.108 · 2009 · External reference
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter
10.1101/gr.214346.116 · 2017 · External reference
ALLPATHS: De novo assembly of whole-genome shotgun microreads
10.1101/gr.7337908 · 2008 · External reference
BASE: a practical de novo assembler for large genomes using long NGS reads
10.1186/s12864-016-2829-5 · 2016 · External reference
Aggressive assembly of pyrosequencing reads with mates
10.1093/bioinformatics/btn548 · 2008 · External reference
De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
10.1101/gr.072033.107 · 2008 · External reference
EPGA: de novo assembly using the distributions of reads and insert size
10.1093/bioinformatics/btu762 · 2014 · External reference
Short read fragment assembly of bacterial genomes
10.1101/gr.7088808 · 2007 · External reference
Gossamer -- a resource-efficient de novo assembler
10.1093/bioinformatics/bts297 · 2012 · External reference
IDBA – A Practical Iterative de Bruijn Graph De Novo Assembler
10.1007/978-3-642-12683-3_28 · 2010 · External reference
ISEA: Iterative Seed-Extension Algorithm for De Novo Assembly Using Paired-End Information and Insert Size Distribution
10.1109/tcbb.2016.2550433 · 2017 · External reference
Assembler for de novo assembly of large genomes
10.1073/pnas.1314090110 · 2013 · External reference
LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads
10.1093/bioinformatics/btw470 · 2016 · External reference
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
10.1371/journal.pone.0023501 · 2011 · External reference
Unresolved reference
2012 · External reference
PCAP: A Whole-Genome Assembly Program
10.1101/gr.1390403 · 2003 · External reference
PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead Approach
10.1371/journal.pone.0114253 · 2014 · External reference
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
10.1101/gr.170720.113 · 2014 · External reference
PE-Assembler: de novo assembler using short paired-end reads
10.1093/bioinformatics/btq626 · 2011 · External reference
QSRA – a quality-value guided de novo short read assembler
10.1186/1471-2105-10-69 · 2009 · External reference
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies
10.1089/cmb.2009.0238 · 2010 · External reference
Readjoiner: a fast and memory efficient string graph-based sequence assembler
10.1186/1471-2105-13-82 · 2012 · External reference
Efficient de novo assembly of large genomes using compressed data structures
10.1101/gr.126953.111 · 2011 · External reference
SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
10.1101/gr.6435207 · 2007 · External reference
De novo assembly of human genomes with massively parallel short read sequencing
10.1101/gr.097261.109 · 2009 · External reference
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
10.1186/2047-217x-1-18 · 2012 · External reference
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
10.1089/cmb.2012.0021 · 2012 · External reference
Exploiting sparseness in de novo genome assembly
10.1186/1471-2105-13-s6-s1 · 2012 · External reference
Assembling millions of short DNA sequences using SSAKE
10.1093/bioinformatics/btl629 · 2006 · External reference
A fast hybrid short read fragment assembly algorithm
10.1093/bioinformatics/btp374 · 2009 · External reference
Extending assembly of short DNA sequences to handle error
10.1093/bioinformatics/btm451 · 2007 · External reference
Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies
10.1002/0471250953.bi1105s31 · 2010 · External reference
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
10.1101/gr.215087.116 · 2017 · External reference
Phased diploid genome assembly with single-molecule real-time sequencing
10.1038/nmeth.4035 · 2016 · External reference
Assembly of long, error-prone reads using repeat graphs
10.1038/s41587-019-0072-8 · 2019 · External reference
HINGE: long-read assembly achieves optimal repeat resolution
10.1101/gr.216465.116 · 2017 · External reference
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
10.1038/nmeth.4432 · 2017 · External reference
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
10.1093/bioinformatics/btw152 · 2016 · External reference
Efficient assembly of nanopore reads via highly accurate and intact error correction
10.1038/s41467-020-20236-7 · 2021 · External reference
Unresolved reference
2019 · External reference
Yet another de novo genome assembler
10.1109/ispa.2019.8868909 · 2019 · External reference
Time- and memory-efficient genome assembly with Raven
10.1038/s43588-021-00073-4 · 2021 · External reference
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
10.1038/s41587-020-0503-6 · 2020 · External reference
SMARTdenovo: a de novo assembler using long noisy reads
10.46471/gigabyte.15 · 2021 · External reference
Unresolved reference
2016 · External reference
Fast and accurate long-read assembly with wtdbg2
10.1038/s41592-019-0669-3 · 2019 · External reference
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
10.1101/gr.263566.120 · 2020 · External reference
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
10.1038/s41592-020-01056-5 · 2021 · External reference
Unresolved reference
2018 · External reference
LJA: Assembling Long and Accurate Reads Using Multiplex de Bruijn GraphsLJA: Assembling long and accurate reads using multiplex de Bruijn graphs
10.1101/2020.12.10.420448 · 2021 · External reference
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer
10.1016/j.cels.2021.08.009 · 2021 · External reference
MBG: Minimizer-based sparse de Bruijn Graph construction
10.1093/bioinformatics/btab004 · 2021 · External reference
Human genome assembly in 100 minutes
10.1101/705616 · 2019 · External reference
A greedy approximation algorithm for constructing shortest common superstrings
10.1016/0304-3975(88)90167-3 · 1988 · External reference
NOVOPlasty: de novo assembly of organelle genomes from whole genome data
10.1093/nar/gkw955 · 2017 · External reference
A strategy of DNA sequencing employing computer programs
10.1093/nar/6.7.2601 · 1979 · External reference
The Sequence of the Human Genome
10.1126/science.1058040 · 2001 · External reference
A Combinatorial Problem
1946 · External reference
48
1894 · External reference
How to apply de Bruijn graphs to genome assembly
10.1038/nbt.2023 · 2011 · External reference
A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome
10.1073/pnas.1909907117 · 2020 · External reference
An evolutionarily-conserved Wnt3/β-catenin/Sp5 feedback loop restricts head organizer activity in Hydra
10.1038/s41467-018-08242-2 · 2019 · External reference
Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?
10.1371/journal.pbio.1001388 · 2012 · External reference
Unresolved reference
2017 · External reference
CoLoRMap: Correcting Long Reads by Mapping short reads
10.1093/bioinformatics/btw463 · 2016 · External reference
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
10.1093/nar/gky724 · 2018 · External reference
Hybrid correction of highly noisy long reads using a variable-order de Bruijn graph
10.1093/bioinformatics/bty521 · 2018 · External reference
Jabba: hybrid error correction for long sequencing reads
10.1186/s13015-016-0075-7 · 2016 · External reference
LoRDEC: accurate and efficient long read error correction
10.1093/bioinformatics/btu538 · 2014 · External reference
Accurate self-correction of errors in long reads using de Bruijn graphs
10.1093/bioinformatics/btw321 · 2017 · External reference
Genome assembly using Nanopore-guided long and error-free DNA reads
10.1186/s12864-015-1519-z · 2015 · External reference
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
10.1093/bioinformatics/btu392 · 2014 · External reference
Scalable long read self-correction and assembly polishing with multiple sequence alignment
10.1038/s41598-020-80757-5 · 2021 · External reference
Non Hybrid Long Read Consensus Using Local De Bruijn Graph Assembly
10.1101/106252 · 2017 · External reference
FLAS: fast and high-throughput algorithm for PacBio long-read self-correction
10.1093/bioinformatics/btz206 · 2019 · External reference
HALC: High throughput algorithm for long read error correction
10.1186/s12859-017-1610-3 · 2017 · External reference
ntEdit: scalable genome sequence polishing
10.1093/bioinformatics/btz400 · 2019 · External reference
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
10.1371/journal.pone.0112963 · 2014 · External reference
The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies
10.1371/journal.pcbi.1007981 · 2020 · External reference
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm
10.1093/bioinformatics/btaa179 · 2020 · External reference
Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads
10.1093/nargab/lqab034 · 2021 · External reference
“HyPo : super fast & accurate polisher for long read assemblies
10.1101/2019.12.19.882506 · 2019 · External reference
Fast and accurate de novo genome assembly from long uncorrected reads
10.1101/gr.214270.116 · 2017 · External reference
Unresolved reference
2014 · External reference
Unresolved reference
2014 · External reference
NextPolish: a fast and efficient genome polishing tool for long-read assembly
10.1093/bioinformatics/btz891 · 2019 · External reference
Unresolved reference
2014 · External reference
HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly
10.1093/bioinformatics/btx220 · 2017 · External reference
Identifying and removing haplotypic duplication in primary genome assemblies
10.1093/bioinformatics/btaa025 · 2020 · External reference
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
10.1186/s12859-018-2485-7 · 2018 · External reference
Hierarchical Scaffolding With Bambus
10.1101/gr.1536204 · 2004 · External reference
Solving scaffolding problem with repeats
10.1101/330472 · 2018 · External reference
BESST - Efficient scaffolding of large fragmented assemblies
10.1186/1471-2105-15-281 · 2014 · External reference
BOSS: a novel scaffolding algorithm based on an optimized scaffold graph
10.1093/bioinformatics/btw597 · 2016 · External reference
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies
10.1093/bioinformatics/bts175 · 2012 · External reference
Fast scaffolding with small independent mixed integer programs
10.1093/bioinformatics/btr562 · 2011 · External reference
Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences
10.1089/cmb.2011.0170 · 2011 · External reference
ScaffMatch: scaffolding algorithm based on maximum weight matching
10.1093/bioinformatics/btv211 · 2015 · External reference
ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction
10.1093/bioinformatics/btv548 · 2016 · External reference
SCARPA: scaffolding reads with practical algorithms
10.1093/bioinformatics/bts716 · 2012 · External reference
SCOP: a novel scaffolding algorithm based on contig classification and optimization
10.1093/bioinformatics/bty773 · 2018 · External reference
SLIQ: Simple Linear Inequalities for Efficient Contig Scaffolding
10.1089/cmb.2011.0263 · 2012 · External reference
SOPRA: Scaffolding algorithm for paired reads via statistical optimization
10.1186/1471-2105-11-345 · 2010 · External reference
Scaffolding pre-assembled contigs using SSPACE
10.1093/bioinformatics/btq683 · 2010 · External reference
WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data
10.1186/s12859-015-0705-y · 2015 · External reference
DENTIST — using long reads for closing assembly gaps at high accuracy
10.1093/gigascience/giab100 · 2022 · External reference
Gapless provides combined scaffolding, gap filling and assembly correction with long readsGapless provides combined scaffolding, gap filling and assembly correction with long reads
10.1101/2022.03.08.483466 · 2022 · External reference
LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads
10.1186/s13742-015-0076-3 · 2015 · External reference
LRScaf: improving draft genomes using long noisy reads
10.1186/s12864-019-6337-2 · 2019 · External reference
Scaffolding and completing genome assemblies in real-time with nanopore sequencing
10.1038/ncomms14515 · 2017 · External reference
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
10.1371/journal.pone.0047768 · 2012 · External reference
10.21105/joss.00116 · 2016 · Admitted local publication
SLR: a scaffolding algorithm based on long reads and contig classification
10.1186/s12859-019-3114-9 · 2019 · External reference
Unresolved reference
2015 · External reference
Single molecule sequencing-guided scaffolding and correction of draft assemblies
10.1186/s12864-017-4271-8 · 2017 · External reference
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information
10.1186/1471-2105-15-211 · 2014 · External reference
ALLMAPS: robust scaffold ordering based on multiple maps
10.1186/s13059-014-0573-1 · 2015 · External reference
AGORA: Assembly Guided by Optical Restriction Alignment
10.1186/1471-2105-13-189 · 2012 · External reference
BiSCoT: improving large eukaryotic genome assemblies with optical maps
10.7717/peerj.10150 · 2020 · External reference
OMGS: Optical Map-Based Genome Scaffolding
10.1089/cmb.2019.0310 · 2020 · External reference
Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool
10.1186/s12864-015-1911-8 · 2015 · External reference
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
10.1093/bioinformatics/btn102 · 2008 · External reference
ARBitR: an overlap-aware genome assembly scaffolder for linked reads
10.1093/bioinformatics/btaa975 · 2020 · External reference
Genome assembly from synthetic long read clouds
10.1093/bioinformatics/btw267 · 2016 · External reference
ARCS: scaffolding genome drafts with linked reads
10.1093/bioinformatics/btx675 · 2017 · External reference
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers
10.1186/s12859-018-2243-x · 2018 · External reference
In vitro, long-range sequence information for de novo genome assembly via transposase contiguity
10.1101/gr.178319.114 · 2014 · External reference
Unresolved reference
2018 · External reference
High-throughput genome scaffolding from in vivo DNA interaction frequency
10.1038/nbt.2768 · 2013 · External reference
High-quality genome (re)assembly using chromosomal contact data
10.1038/ncomms6695 · 2014 · External reference
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling
10.1101/gad.328971.119 · 2019 · External reference
instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder
10.1186/s13059-020-02041-z · 2020 · External reference
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
10.1038/nbt.2727 · 2013 · External reference
Efficient iterative Hi-C scaffolder based on N-best neighbors
10.1186/s12859-021-04453-5 · 2021 · External reference
Scaffolding of long read assemblies using long range contact information
10.1186/s12864-017-3879-z · 2017 · External reference
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
10.1371/journal.pcbi.1007273 · 2019 · External reference
Unresolved reference
2019 · External reference
YaHS: yet another Hi-C scaffolding tool. Version v1.1a
10.5281/zenodo.5848773 · 2021 · External reference
Toward almost closed genomes with GapFiller
10.1186/gb-2012-13-6-r56 · 2012 · External reference
GAPPadder: a sensitive approach for closing gaps on draft genomes with short sequence reads
10.1186/s12864-019-5703-4 · 2019 · External reference
Sealer: a scalable gap-closing application for finishing draft genomes
10.1186/s12859-015-0663-4 · 2015 · External reference
FGAP: an automated gap closing tool
10.1186/1756-0500-7-371 · 2014 · External reference
GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments
10.1093/bioinformatics/btv465 · 2015 · External reference
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
10.1093/gigascience/giy157 · 2019 · External reference
PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes
10.1177/1176934320913859 · 2020 · External reference
TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads
10.1093/gigascience/giaa094 · 2020 · External reference
Sequencing DNA with nanopores: Troubles and biases
10.1371/journal.pone.0257521 · 2021 · External reference
Long-read error correction: a survey and qualitative comparisonLong-read error correction: a survey and qualitative comparison
10.1101/2020.03.06.977975 · 2020 · External reference
Widespread false gene gains caused by duplication errors in genome assembliesWidespread false gene gains caused by duplication errors in genome assemblies
10.1101/2021.04.09.438957 · 2021 · External reference
Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms
10.1186/s12859-021-04118-3 · 2021 · External reference
Assembly of the Working Draft of the Human Genome with GigAssembler
10.1101/gr.183201 · 2001 · External reference
Modern technologies and algorithms for scaffolding assembled genomes
10.1371/journal.pcbi.1006994 · 2019 · External reference
Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools
10.3389/fgene.2015.00220 · 2015 · External reference
Ordered Restriction Maps of Saccharomyces cerevisiae Chromosomes Constructed by Optical Mapping
10.1126/science.8211116 · 1993 · External reference
A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni
10.1371/journal.pntd.0001455 · 2012 · External reference
The genome of the harpacticoid copepod Tigriopus japonicus: Potential for its use in marine molecular ecotoxicology
10.1016/j.aquatox.2020.105462 · 2020 · External reference
10.1016/j.csbj.2020.07.018 · 2020 · Admitted local publication
The genome of Onchocerca volvulus, agent of river blindness
10.1038/nmicrobiol.2016.216 · 2016 · External reference
Comparative genome analysis of programmed DNA elimination in nematodes
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Unresolved reference
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Capturing Chromosome Conformation
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10.1016/j.febslet.2015.04.034 · 2015 · External reference
Three invariant Hi-C interaction patterns: Applications to genome assembly
10.1016/j.ymeth.2018.04.013 · 2018 · External reference
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The MaSuRCA genome assembler
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Efficient hybrid de novo assembly of human genomes with WENGAN
10.1038/s41587-020-00747-w · 2020 · External reference
First estimates of genome size in ribbon worms (phylum Nemertea) using flow cytometry and Feulgen image analysis densitometry
10.1139/cjz-2014-0068 · 2014 · External reference
Unresolved reference
2013 · External reference
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
10.1038/s41467-020-14998-3 · 2020 · External reference
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
10.1093/bioinformatics/btw663 · 2016 · External reference
Mapping-based genome size estimationMapping-based genome size estimation
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QUAST: quality assessment tool for genome assemblies
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BlobTools: Interrogation of genome assemblies
10.12688/f1000research.12232.1 · 2017 · External reference
BlobToolKit – Interactive Quality Assessment of Genome Assemblies
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Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade
10.1073/pnas.1510461112 · 2015 · External reference
No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini
10.1073/pnas.1600338113 · 2016 · External reference
10.1016/j.csbj.2019.11.011 · 2020 · Admitted local publication
De novo assembly of haplotype-resolved genomes with trio binning
10.1038/nbt.4277 · 2018 · External reference
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
10.1101/gr.213462.116 · 2016 · External reference
WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads
10.1089/cmb.2014.0157 · 2015 · External reference
Unresolved reference
2017 · External reference
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10.1038/s41467-019-09575-2 · 2019 · External reference
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
10.1038/s41587-020-0719-5 · 2020 · External reference
Haplotype-resolved genome analyses of a heterozygous diploid potato
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Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly
10.1186/s13059-020-02244-4 · 2021 · External reference
Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data
10.1038/s41477-019-0487-8 · 2019 · External reference
GraphUnzip: unzipping assembly graphs with long reads and Hi-CGraphUnzip: unzipping as- sembly graphs with long reads and Hi-C
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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C
10.1038/s41467-020-20536-y · 2021 · External reference
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
10.1186/s13059-020-02134-9 · 2020 · External reference
Next-generation genome annotation: we still struggle to get it right
10.1186/s13059-019-1715-2 · 2019 · External reference
The FAIR Guiding Principles for scientific data management and stewardship
10.1038/sdata.2016.18 · 2016 · External reference
Unresolved reference
External reference
Unresolved reference
2022 · External reference
Unresolved reference
2022 · External reference
