Fast and accurate long-read assembly with wtdbg2

By Jue Ruan, Heng Li. Nature Methods, 2019

1,123 citations recorded by the source corpus.

Existing long-read assemblers require thousands of central processing unit hours to assemble a human genome and are being outpaced by sequencing technologies in terms of both throughput and cost. We developed a long-read assembler wtdbg2 (https://github.com/ruanjue/wtdbg2) that is 2–17 times as fast as published tools while achieving comparable contiguity and accuracy. It paves the way for population-scale long-read assembly in future. Wtdbg2 assembles genomes with comparable contiguity and accuracy to existing tools using long-read sequencing data, and is several times faster, especially for large genomes.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2022788629b17f6d89b9f8d789119949f03b4365

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Citations in the corpus

Time- and memory-efficient genome assembly with Raven (2021, methodology): “Because of resource limitations, we chose the best-performing genome assemblers for erroneous third-generation data from recent scientific papers 3,6,16 .”
Opportunities and challenges in long-read sequencing data analysis (2020, background): “Filtering out these rare k-mers, as the wtdbg2 assembler does [63], effectively prevents errors from being introduced in the assembly (Fig.”
NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads (2024, background): “…and then corrects errors in the assembled genome); the former (such as Necat [14] and Canu [15]) is usually slower than the latter (such as Wtdbg2 [16] and Flye [17]), because read-level error correction requires much more computational resources than contig-level polishing (a step to correct…”
Long-read human genome sequencing and its applications (2020, neutral): “This more than 100-fold increase in assembly 74 , FALCON 75 , Flye 76 , wtdbg2 (or RedBean) 77 and Shasta 36 ) and other tools that can increase assembly .”
Nanopore sequencing technology, bioinformatics and applications (2021, methodology): “The recently developed assembler wtdbg2 runs much faster than other tools without sacrificing contiguity and accuracy 111 .”
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome (2019, methodology): “Three different algorithms— FALCON 39 , Canu 40 and wtdbg2 41 —were used to assemble the full CCS read set, which is a mix of paternal and maternal reads.”