Space-efficient and exact de Bruijn graph representation based on a Bloom filter
Rayan Chikhi,Guillaume Rizk +1 more
TLDR
A new encoding of the de Bruijn graph, which occupies an order of magnitude less space than current representations, is proposed, which performed a complete de novo assembly of human genome short reads using 5.7 GB of memory in 23 hours.Abstract:
The de Bruijn graph data structure is widely used in next-generation sequencing (NGS). Many programs, e.g. de novo assemblers, rely on in-memory representation of this graph. However, current techniques for representing the de Bruijn graph of a human genome require a large amount of memory (≥30 GB). We propose a new encoding of the de Bruijn graph, which occupies an order of magnitude less space than current representations. The encoding is based on a Bloom filter, with an additional structure to remove critical false positives. An assembly software implementing this structure, Minia, performed a complete de novo assembly of human genome short reads using 5.7 GB of memory in 23 hours.read more
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MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
TL;DR: MEGAHIT as mentioned in this paper is a NGS de novo assembler for assembling large and complex metagenomics data in a time and cost-efficient manner, which avoids preprocessing like partitioning and normalization, which might compromise on result integrity.
Journal ArticleDOI
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
Dinghua Li,Ruibang Luo,Chi-Man Liu,Chi-Ming Leung,Hing-Fung Ting,Kunihiko Sadakane,Hiroshi Yamashita,Tak-Wah Lam +7 more
TL;DR: The details of the core algorithms in MEG AHIT v0.1 are described, and the new modules to upgrade MEGAHIT to version v1.0 are shown, which gives better assembly quality, runs faster and uses less memory.
Journal ArticleDOI
Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software
Alexander Sczyrba,Peter Hofmann,Peter Hofmann,Peter Belmann,David Koslicki,Stefan Janssen,Johannes Dröge,Johannes Dröge,Ivan Gregor,Ivan Gregor,Stephan Majda,Jessika Fiedler,Eik Dahms,Eik Dahms,Andreas Bremges,Adrian Fritz,Ruben Garrido-Oter,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Nicole Shapiro,Philip D. Blood,Alexey Gurevich,Yang Bai,Dmitrij Turaev,Matthew Z. DeMaere,Rayan Chikhi,Niranjan Nagarajan,Christopher Quince,Fernando Meyer,Monika Balvočiūtė,Lars Hestbjerg Hansen,Søren J. Sørensen,Burton Kuan Hui Chia,Bertrand Denis,Jeff Froula,Zhong Wang,Robert Egan,Dongwan Don Kang,Jeffrey J. Cook,Charles Deltel,Michael Beckstette,Claire Lemaitre,Pierre Peterlongo,Guillaume Rizk,Dominique Lavenier,Yu Wei Wu,Yu Wei Wu,Steven W. Singer,Steven W. Singer,Chirag Jain,Marc Strous,Heiner Klingenberg,Peter Meinicke,Michael D. Barton,Thomas Lingner,Hsin-Hung Lin,Yu-Chieh Liao,Genivaldo G. Z. Silva,Daniel A. Cuevas,Robert Edwards,Surya Saha,Vitor C. Piro,Vitor C. Piro,Bernhard Y. Renard,Mihai Pop,Hans-Peter Klenk,Markus Göker,Nikos C. Kyrpides,Tanja Woyke,Julia A. Vorholt,Paul Schulze-Lefert,Edward M. Rubin,Aaron E. Darling,Thomas Rattei,Alice C. McHardy +75 more
TL;DR: The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups as discussed by the authors.
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LoRDEC: accurate and efficient long read error correction.
Leena Salmela,Eric Rivals +1 more
TL;DR: LoRDEC, a hybrid error correction method that builds a succinct de Bruijn graph representing the short reads, and seeks a corrective sequence for each erroneous region in the long reads by traversing chosen paths in the graph is presented.
Posted Content
Informed and Automated k-Mer Size Selection for Genome Assembly
Rayan Chikhi,Paul Medvedev +1 more
TL;DR: A fast and accurate sampling method is developed that constructs approximate abundance histograms with several orders of magnitude performance improvement over traditional methods and a fast heuristic is presented that uses the generated abundance histogram for putative k values to estimate the best possible value of k.
References
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Journal ArticleDOI
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred Grabherr,Brian J. Haas,Moran Yassour,Moran Yassour,Joshua Z. Levin,Dawn Thompson,Ido Amit,Xian Adiconis,Lin Fan,Raktima Raychowdhury,Qiandong Zeng,Zehua Chen,Evan Mauceli,Nir Hacohen,Andreas Gnirke,Nicholas Rhind,Federica Di Palma,Bruce W. Birren,Chad Nusbaum,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Nir Friedman,Aviv Regev +22 more
TL;DR: The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
Journal ArticleDOI
ABySS: A parallel assembler for short read sequence data
Jared T. Simpson,Kim Wong,Shaun D. Jackman,Jacqueline E. Schein,Steven J.M. Jones,Inanc Birol +5 more
TL;DR: ABySS (Assembly By Short Sequences), a parallelized sequence assembler, was developed and assembled 3.5 billion paired-end reads from the genome of an African male publicly released by Illumina, Inc, representing 68% of the reference human genome.
Journal ArticleDOI
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
Guillaume Marçais,Carl Kingsford +1 more
TL;DR: This work proposes a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient, based on a multithreaded, lock-free hash table optimized for counting k-mers up to 31 bases in length.
Journal ArticleDOI
De novo assembly of human genomes with massively parallel short read sequencing
Ruiqiang Li,Hongmei Zhu,Jue Ruan,Wubin Qian,Xiaodong Fang,Zhongbin Shi,Yingrui Li,Shengting Li,Gao Shan,Karsten Kristiansen,Songgang Li,Huanming Yang,Jing Wang,Jun Wang +13 more
TL;DR: The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way.
Journal ArticleDOI
Assembly algorithms for next-generation sequencing data.
TL;DR: This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo to compare the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly.
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Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more