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
Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China
Yu-Rong Liu,Yu-Rong Liu,Manuel Delgado-Baquerizo,Manuel Delgado-Baquerizo,Li Bi,Jun Zhu,Ji-Zheng He,Ji-Zheng He +7 more
TL;DR: The results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.
Journal ArticleDOI
Bisphenol A alters gut microbiome: Comparative metagenomics analysis.
TL;DR: The effects of dietary BPA intake on the shift of microbial community structure were similar to those of a HFD and HSD, and revealed microbial markers for the development of diseases associated with an unstable microbiota.
Journal ArticleDOI
Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants.
Julia Hassa,Irena Maus,Sandra Off,Alfred Pühler,Paul Scherer,Michael Klocke,Andreas Schlüter +6 more
TL;DR: Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters, and metatranscriptome sequencing provided insights into the metabolically active community.
Journal ArticleDOI
One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers
Karen Smith,Andrew Collier,Eleanor M. Townsend,Eleanor M. Townsend,Lindsay E. O'Donnell,Abhijit M. Bal,John Butcher,William G. Mackay,Gordon Ramage,Craig Williams +9 more
TL;DR: The abundance of anaerobic bacteria has important implications for treatment as it suggests that the microbiome of each ulcer “starts afresh” and that the duration of current ulceration may be a more important consideration than a history of healed ulcer.
Journal ArticleDOI
APOE genotype influences the gut microbiome structure and function in humans and mice: relevance for Alzheimer’s disease pathophysiology
Tam T. T. Tran,Simone Corsini,Lee Kellingray,Claire Hegarty,Gwénaëlle Le Gall,Arjan Narbad,Michael Müller,Noemi Tejera,Paul W. O'Toole,Anne Marie Minihane,David Vauzour +10 more
TL;DR: The findings indicate that APOE genotype is associated with specific gut microbiome profiles in both humans and APOE‐TR mice, and suggests that the gut microbiome is worth further investigation as a potential target to mitigate the deleterious impact of the APOE4 allele on cognitive decline and the prevention of AD.
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