Results 21 to 30 of about 724,062 (300)

Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine [PDF]

, 2019
Background: Mycobacterium bovis bacillus Calmette-Guerin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Russia BCG-1 were
Borgers, Katlyn, Callewaert, Nico, Festjens, Nele, Lin, Yao-Cheng, Michielsen, Gitte, Ou, Jheng-Yang, Plets, Evelyn, Tiels, Petra, Van Hecke, Annelies, Zheng, Po-Xing   +9 more
core   +2 more sources

Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion [PDF]

, 2018
The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades.
De Vrieze, Jo, Ijaz, Umer Z., Saunders, Aaron M., Theuerl, Susanne   +3 more
core   +6 more sources

A Hybrid Sequencing Approach Completes the Genome Sequence of Thermoanaerobacter ethanolicus JW 200 [PDF]

, 2019
Thermoanaerobacter ethanolicus JW 200 has been identified as a potential sustainable biofuel producer due to its ability to readily ferment carbohydrates to ethanol. A hybrid sequencing approach, combining Oxford Nanopore and Illumina DNA sequence reads,
Ayine, Monica L., Gill, Steven R., Gilman, James A., Hewlett, Mark, James, Paul B.C., Love, John, Parker, David A., Power, Ann L., Singleton, Chloe, Tennant, Richard K.   +9 more
core   +1 more source

Statistical issues in the analysis of Illumina data [PDF]

BMC Bioinformatics, 2008
Illumina bead-based arrays are becoming increasingly popular due to their high degree of replication and reported high data quality. However, little attention has been paid to the pre-processing of Illumina data. In this paper, we present our experience of analysing the raw data from an Illumina spike-in experiment and offer guidelines for those ...
Mark J. Dunning, Nuno L. Barbosa-Morais, Andy G. Lynch, Simon Tavaré, Matthew E. Ritchie   +4 more
openaire   +4 more sources

An improved protocol for small RNA library construction using High Definition adapters [PDF]

, 2015
Next generation sequencing of small RNA (sRNA) libraries is widely used for studying sRNAs in various biological systems. However, cDNA libraries of sRNAs are biased for molecules that are ligated to adapters more or less efficiently than other molecules.
Aravin, Baran, Bushati, Edgar, Git, Hafner, He, Jagadeeswaran, Jayaprakash, Kawano, Mallory, Mortazavi, Munafó, Pease, Prüfer, Raabe, Reddy, Song, Sorefan, Stocks, Sun, Szittya, Szittya, Tian, Vigneault, Viollet, Willenbrock, Zhang, Zhuang   +28 more
core   +1 more source

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm [PDF]

, 2020
The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C.
Al Hakimi, Amin, Bentley, Nolan, Bertrand, Benoît, Cattonaro, Frederica, Cerutti, Mario, Del Terra, Lorenzo, Di Gaspero, Gabriele, Graziosi, Giorgio, Jurman, Irena, Klein, Patricia E., Magni, Federica, Magris, Gabriele, Montagnon, Christophe, Morgante, Michele, Murray, Seth C., Navarini, Luciano, Pallavicini, Alberto, Pellegrino, Gloria, Pinosio, Sara, Ruosi, Manuela Rosanna, Scaglione, Davide, Scalabrin, Simone, Schilling, Timothy, Solano, William, Suggi Liverani, Furio, Toniutti, Lucile, Valle, Giorgio, Vidotto, Michele, Vitulo, Nicola   +28 more
core   +3 more sources

QuorUM: An Error Corrector for Illumina Reads

PLOS ONE, 2015
Motivation: Illumina Sequencing data can provide high coverage of a genome by relatively short (100 bp150 bp) reads at a low cost. Our goal is to produce trimmed and error-corrected reads to improve genome assemblies. Our error correction procedure aims at producing a set of error-corrected reads (1) minimizing the number of distinct false k-mers, i.e.
Guillaume Marçais, James A Yorke, Aleksey Zimin   +2 more
openaire   +4 more sources

Quality Control for the Illumina HumanExome BeadChip [PDF]

Current Protocols in Human Genetics, 2016
AbstractThe Illumina HumanExome BeadChip and other exome‐based genotyping arrays offer inexpensive genotyping of some 240,000 mostly nonsynonymous coding variants across the human genome. The HumanExome chip, with its highly non‐uniform distribution of markers and emphasis on rare coding variants, presents some unique challenges for quality control (QC)
Robert P, Igo, Jessica N, Cooke Bailey, Jane, Romm, Jonathan L, Haines, Janey L, Wiggs   +4 more
openaire   +2 more sources

NxRepair: error correction in de novo sequence assembly using Nextera mate pairs [PDF]

PeerJ, 2015
Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding ...
Rebecca R. Murphy, Jared O’Connell, Anthony J. Cox, Ole Schulz-Trieglaff   +3 more
doaj   +2 more sources

A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments. [PDF]

, 2017
BackgroundPCR amplification is an important step in the preparation of DNA sequencing libraries prior to high-throughput sequencing. PCR amplification introduces redundant reads in the sequence data and estimating the PCR duplication rate is important to
Bansal, Vikas
core   +2 more sources