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
The gut microbiome is associated with behavioural task in honey bees
Julia C. Jones,Julia C. Jones,Carmelo Fruciano,Carmelo Fruciano,J. Marchant,Falk Hildebrand,Sofia K. Forslund,Peer Bork,Philipp Engel,William O. H. Hughes +9 more
TL;DR: The authors' results show that some core members of the unique honey bee gut bacterial community are represented in different relative abundances in bees performing different behavioural tasks, and suggest an influence of task-related local environment exposure and diet on the honey bees gut microbial community.
Journal ArticleDOI
Oceanographic boundaries constrain microbial diversity gradients in the south pacific ocean
Eric J Raes,Eric J Raes,Eric J Raes,Levente Bodrossy,Jodie van de Kamp,Andrew Bissett,Martin Ostrowski,Mark V. Brown,Swan Li San Sow,Swan Li San Sow,Bernadette M. Sloyan,Anya M. Waite,Anya M. Waite +12 more
TL;DR: It is shown that temperature does not determine patterns of marine microbial richness, and permanent oceanographic features, such as the STF and the equatorial upwelling, can have a significant influence on both alpha-diversity and beta-d diversity of pro- and eukaryotes.
Journal ArticleDOI
The salivary microbiome for differentiating individuals: proof of principle.
TL;DR: It is shown that samples from the same person group together regardless of time of sampling, indicating that it is possible to distinguish two people using the bacterial microbiota present in their saliva.
Journal ArticleDOI
No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing.
Catherine J. Westbrook,Julie A. Karl,Roger W. Wiseman,Suzanne Mate,G. I. Koroleva,Karla Garcia,Mariano Sanchez-Lockhart,David H. O’Connor,Gustavo Palacios +8 more
TL;DR: The SMRT-CCS method described here provides a straightforward protocol for characterization of unfragmented single-molecule cDNA transcripts that will potentially revolutionize MHC class I allele discovery in nonhuman primates and other species.
Journal ArticleDOI
Lactobacillus plantarum PFM 105 Promotes Intestinal Development Through Modulation of Gut Microbiota in Weaning Piglets.
Tianwei Wang,Kunling Teng,Yayong Liu,Weixiong Shi,Jie Zhang,Dong Enqiu,Xin Zhang,Yong Tao,Jin Zhong +8 more
TL;DR: It is demonstrated here that L. plantarum PFM 105 could promote intestinal development through modulation of gut microbiota in weaning piglets through significantly increase the relative abundance of metabolic genes which may important to intestinal microbiota maturation.
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