FLASH: Fast Length Adjustment of Short Reads to Improve Genome Assemblies
Tanja Magoc,Steven L. Salzberg +1 more
TLDR
FLASH is a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short and when FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.Abstract:
Motivation: Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome.
Results: We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.
Availability and Implementation: The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash.
Contact: moc.liamg@cogam.tread more
Citations
More filters
Enrichment Dynamics of Listeria monocytogenes and the Associated Microbiome from Naturally Contaminated Ice Cream Linked to a Listeriosis Outbreak
TL;DR: In this paper, the dynamics of co-enriching microbiota during recovery of Listeria monocytogenes from naturally contaminated ice cream samples linked to an outbreak are described for three different initial enrichment formulations used by the Food and Drug Administration (FDA), the International Organization of Standardization (ISO), and the United States Department of Agriculture (USDA).
Journal ArticleDOI
Metagenomic and metatranscriptomic insights into the complex nitrogen metabolic pathways in a single-stage bioreactor coupling partial denitrification with anammox
TL;DR: The nitrogen metabolic network is established based on the comprehensive analyses of the abundance and mRNA expression of functional genes, which might improve the understanding of the nitrogen metabolic mechanisms of the combined partial-denitrification and anammox process.
Journal ArticleDOI
Genetic code expansion for multiprotein complex engineering
Christine Koehler,Paul F. Sauter,Mirella Wawryszyn,Gemma Estrada Girona,Kapil Gupta,Jonathan J M Landry,Markus Hsi-Yang Fritz,Ksenija Radic,Jan Erik Hoffmann,Zhuo Angel Chen,Juan Zou,Piau Siong Tan,Bence Galik,Sini Junttila,Peggy Stolt-Bergner,Giancarlo Pruneri,Attila Gyenesei,Carsten Schultz,Moritz Bosse Biskup,Hueseyin Besir,Vladimir Benes,Juri Rappsilber,Juri Rappsilber,Martin Jechlinger,Jan O. Korbel,Imre Berger,Imre Berger,Stefan Braese,Edward A. Lemke +28 more
TL;DR: The versatility of this efficient and robust protein production platform, 'MultiBacTAG', is demonstrated for the fluorescent labeling of target proteins and biologics using click chemistries, for glycoengineering of antibodies, and for structure–function studies of novel eukaryotic complexes.
Journal ArticleDOI
Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents.
Sean M. McAllister,Shawn W. Polson,David A. Butterfield,David A. Butterfield,Brian T. Glazer,Jason B. Sylvan,Clara S. Chan +6 more
TL;DR: Investigating a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, shows that Cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity.
Journal ArticleDOI
Anaerobic ammonium oxidation coupled to iron reduction in constructed wetland mesocosms.
Weitao Shuai,Peter R. Jaffé +1 more
TL;DR: Two constructed wetlands were built and bioaugmented with A6 to determine if, under the right conditions, Feammox can be enhanced in CWs by having strata with higher iron content, indicating that wetlands can be constructed to take advantage of the Feamm ox process for increased NH4+ removal.
References
More filters
Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI
Versatile and open software for comparing large genomes
Stefan Kurtz,Adam M. Phillippy,Arthur L. Delcher,Michael E. Smoot,Martin Shumway,Corina Antonescu,Steven L. Salzberg +6 more
TL;DR: The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes.
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
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
Sante Gnerre,Iain MacCallum,Dariusz Przybylski,Filipe J. Ribeiro,Joshua N. Burton,Bruce J. Walker,Ted Sharpe,Giles Hall,Terrance Shea,Sean M. Sykes,Aaron M. Berlin,Daniel Aird,Maura Costello,Riza M. Daza,Louise Williams,Robert Nicol,Andreas Gnirke,Chad Nusbaum,Eric S. Lander,David B. Jaffe +19 more
TL;DR: The development of an algorithm for genome assembly, ALLPATHS-LG, and its application to massively parallel DNA sequence data from the human and mouse genomes, generated on the Illumina platform, have good accuracy, short-range contiguity, long-range connectivity, and coverage of the genome.
Related Papers (5)
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
Trimmomatic: a flexible trimmer for Illumina sequence data
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more