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
Journal ArticleDOI
Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice
Gaelle Carrat,Ming Hu,Marie-Sophie Nguyen-Tu,Pauline Chabosseau,Kyle J. Gaulton,Kyle J. Gaulton,Martijn van de Bunt,Martijn van de Bunt,Afshan Siddiq,Mario Falchi,Mario Falchi,Matthias Thurner,Matthias Thurner,Mickaël Canouil,François Pattou,Isabelle Leclerc,Timothy J. Pullen,Matthew C. Cane,Priyanka Prabhala,William W. Greenwald,William W. Greenwald,Anke M. Schulte,Piero Marchetti,Mark Ibberson,Patrick E. MacDonald,Jocelyn E. Manning Fox,Anna L. Gloyn,Anna L. Gloyn,Anna L. Gloyn,Philippe Froguel,Michele Solimena,Michele Solimena,Mark I. McCarthy,Mark I. McCarthy,Mark I. McCarthy,Guy A. Rutter +35 more
TL;DR: In this paper, the causal variant(s) at this locus to a 5 kb region that overlaps a stretch-enhancer active in islets were identified and correlated with type 2 diabetes risk.
Journal ArticleDOI
Effects of aeration strategy on the evolution of dissolved organic matter (DOM) and microbial community structure during sludge bio-drying
Junya Zhang,Xing Cai,Lu Qi,Chun-yan Shao,Yang Lin,Jin Zhang,Yuan-li Zhang,Peihong Shen,Yuansong Wei +8 more
TL;DR: The interplay between the DOM and microbial community during sludge bio-drying is elucidated and the microbial community changed significantly at first and subsequently stabilized, and the genus Parapedobacter, which belongs to Bacteriodetes, became dominant.
Journal ArticleDOI
Bacterial communities associated with houseflies (Musca domestica L.) sampled within and between farms
TL;DR: This study is the first in-depth amplicon sequencing study of the housefly microbiota, and collectively shows that the microbiota of single houseflies is highly diverse and differs between individuals likely to reflect the lifestyle of theHousefly.
Journal ArticleDOI
Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants.
TL;DR: Soil pH, P and K significantly affected the composition of the soybean rhizomicrobiome, whereas soil pH and N had a significant effect on the alfalfa rhizome, and the rhizomes assemblage and plant growth-associated microbes are differentially structured by soil properties and leguminous plant species.
Journal ArticleDOI
Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy.
Roberto Berni Canani,Francesca De Filippis,Rita Nocerino,Lorella Paparo,Carmen Di Scala,Linda Cosenza,Giusy Della Gatta,Antonio Calignano,Carmen De Caro,Manolo Laiola,Jack A. Gilbert,Danilo Ercolini +11 more
TL;DR: A gut microbiota dysbiosis is found in non-IgE-mediated CMA, driven by an enrichment of Bacteroides and Alistipes from healthy to IgE- mediated CMA patients, and longitudinal cohort studies in children with CMA will confirm these results.
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