G
Guillaume Marçais
Researcher at Carnegie Mellon University
Publications - 45
Citations - 9490
Guillaume Marçais is an academic researcher from Carnegie Mellon University. The author has contributed to research in topics: Genome & Sequence assembly. The author has an hindex of 22, co-authored 43 publications receiving 7343 citations. Previous affiliations of Guillaume Marçais include Johns Hopkins University School of Medicine & University of Maryland, College Park.
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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.
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MUMmer4: A fast and versatile genome alignment system.
Guillaume Marçais,Arthur L. Delcher,Adam M. Phillippy,Rachel Coston,Steven L. Salzberg,Aleksey V. Zimin,Aleksey V. Zimin +6 more
TL;DR: MUMmer4 is described, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of Mummer to a 48- bit suffix array, and that offers improved speed through parallel processing of input query sequences.
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A whole-genome assembly of the domestic cow, Bos taurus
Aleksey V. Zimin,Arthur L. Delcher,Liliana Florea,David R. Kelley,Michael C. Schatz,Daniela Puiu,Finnian Hanrahan,Geo Pertea,Curtis P. Van Tassell,Tad S. Sonstegard,Guillaume Marçais,Michael Roberts,Poorani Subramanian,James A. Yorke,Steven L. Salzberg +14 more
TL;DR: By using independent mapping data and conserved synteny between the cow and human genomes, this work was able to construct an assembly with excellent large-scale contiguity in which a large majority (approximately 91%) of the genome has been placed onto the 30 B. taurus chromosomes.
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The MaSuRCA genome assembler
Aleksey V. Zimin,Guillaume Marçais,Daniela Puiu,Michael Roberts,Steven L. Salzberg,James A. Yorke +5 more
TL;DR: A new hybrid approach that has the computational efficiency of de Bruijn graph methods and the flexibility of overlap-based assembly strategies, and which allows variable read lengths while tolerating a significant level of sequencing error is described.
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GAGE: A critical evaluation of genome assemblies and assembly algorithms
Steven L. Salzberg,Adam M. Phillippy,Aleksey V. Zimin,Daniela Puiu,Tanja Magoc,Sergey Koren,Sergey Koren,Todd J. Treangen,Michael C. Schatz,Arthur L. Delcher,Michael Roberts,Guillaume Marçais,Mihai Pop,James A. Yorke +13 more
TL;DR: Evaluating several of the leading de novo assembly algorithms on four different short-read data sets generated by Illumina sequencers concludes that data quality, rather than the assembler itself, has a dramatic effect on the quality of an assembled genome.