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WENGAN: Efficient and high quality hybrid de novo assembly of human genomes

https://doi.org/10.1101/840447
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Approximation algorithms for covering a graph by vertex‐disjoint paths of maximum total weight
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LEMON – an Open Source C++ Graph Template Library
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One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
inferredcites →https://doi.org/10.1038/nature07517openalex-snapshot
Accurate whole human genome sequencing using reversible terminator chemistry
inferredcites →https://doi.org/10.1038/nbt.4060openalex-snapshot
Nanopore sequencing and assembly of a human genome with ultra-long reads
inferredcites →https://doi.org/10.1038/ng.3121openalex-snapshot
Comprehensive variation discovery in single human genomes
inferredcites →https://doi.org/10.1038/nmeth.2474openalex-snapshot
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot
A complete bacterial genome assembled de novo using only nanopore sequencing data
inferredcites →https://doi.org/10.1038/nmeth.4035openalex-snapshot
Phased diploid genome assembly with single-molecule real-time sequencing
inferredcites →https://doi.org/10.1038/s41576-018-0003-4openalex-snapshot
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
inferredcites →https://doi.org/10.1038/s41587-018-0004-zopenalex-snapshot
Errors in long-read assemblies can critically affect protein prediction
inferredcites →https://doi.org/10.1038/s41587-019-0072-8openalex-snapshot
Assembly of long, error-prone reads using repeat graphs
inferredcites →https://doi.org/10.1038/s41587-019-0217-9openalex-snapshot
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
inferredcites →https://doi.org/10.1038/s41587-020-0503-6openalex-snapshot
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
inferredcites →https://doi.org/10.1038/s41592-018-0236-3openalex-snapshot
Long-read sequence and assembly of segmental duplications
inferredcites →https://doi.org/10.1038/s41592-019-0669-3openalex-snapshot
Fast and accurate long-read assembly with wtdbg2
inferredcites →https://doi.org/10.1073/pnas.171285098openalex-snapshot
An Eulerian path approach to DNA fragment assembly
inferredcites →https://doi.org/10.1089/cmb.2011.0151openalex-snapshot
Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers
inferredcites →https://doi.org/10.1093/bioinformatics/btg109openalex-snapshot
Generating consensus sequences from partial order multiple sequence alignment graphs
inferredcites →https://doi.org/10.1093/bioinformatics/bth408openalex-snapshot
Reducing storage requirements for biological sequence comparison
inferredcites →https://doi.org/10.1093/bioinformatics/bti1114openalex-snapshot
The fragment assembly string graph
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btw279openalex-snapshot
Compacting de Bruijn graphs from sequencing data quickly and in low memory
inferredcites →https://doi.org/10.1093/bioinformatics/btw753openalex-snapshot
Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance
inferredcites →https://doi.org/10.1093/bioinformatics/btx304openalex-snapshot
KMC 3: counting and manipulating k -mer statistics
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bty266openalex-snapshot
Versatile genome assembly evaluation with QUAST-LG
inferredcites →https://doi.org/10.1093/bioinformatics/btz400openalex-snapshot
ntEdit: scalable genome sequence polishing
inferredcites →https://doi.org/10.1093/gigascience/giw015openalex-snapshot
Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
inferredcites →https://doi.org/10.1093/gigascience/gix024openalex-snapshot
A reference human genome dataset of the BGISEQ-500 sequencer
inferredcites →https://doi.org/10.1093/gigascience/giy048openalex-snapshot
Fast-SG: an alignment-free algorithm for hybrid assembly
inferredcites →https://doi.org/10.1101/051516openalex-snapshot
trio-sga : facilitating de novo assembly of highly heterozygous genomes with parent-child trios
inferredcites →https://doi.org/10.1101/565374openalex-snapshot
ntEdit: scalable genome assembly polishing
inferredcites →https://doi.org/10.1101/gr.213405.116openalex-snapshot
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii , a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm
inferredcites →https://doi.org/10.1101/gr.214270.116openalex-snapshot
Fast and accurate de novo genome assembly from long uncorrected reads
inferredcites →https://doi.org/10.1101/gr.214346.116openalex-snapshot
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1126/science.1162986openalex-snapshot
Real-Time DNA Sequencing from Single Polymerase Molecules
inferredcites →https://doi.org/10.1137/0215009openalex-snapshot
An $O(EV\log V)$ Algorithm for Finding a Maximal Weighted Matching in General Graphs
inferredcites →https://doi.org/10.1145/585265.585267openalex-snapshot
The greedy path-merging algorithm for contig scaffolding
inferredcites →https://doi.org/10.1186/1748-7188-8-22openalex-snapshot
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
inferredcites →https://doi.org/10.1186/s13059-016-1103-0openalex-snapshot
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s10142-021-00810-yopenalex-snapshot
Music of metagenomics—a review of its applications, analysis pipeline, and associated tools
inferred← citeshttps://doi.org/10.1016/j.isci.2020.101389openalex-snapshot
HASLR: Fast Hybrid Assembly of Long Reads
inferred← citeshttps://doi.org/10.1101/2021.02.17.431362openalex-snapshot
Ancient Migrations - The first complete genome assembly, annotation and variants of the Zoroastrian-Parsi community of India
inferred← citeshttps://doi.org/10.1101/2021.09.07.459217openalex-snapshot
GABOLA: A Reliable Gap-Filling Strategy for de novo Chromosome-Level Assembly
inferred← citeshttps://doi.org/10.1186/s12915-021-01158-2openalex-snapshot
The transposable element-rich genome of the cereal pest Sitophilus oryzae
inferred← citeshttps://doi.org/10.1186/s13015-021-00186-5openalex-snapshot
LazyB: fast and cheap genome assembly
inferred← citeshttps://doi.org/10.3892/mmr.2021.11890openalex-snapshot
Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly
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