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khmer release v2.1: software for biological sequence analysis

Daniel Standage, Ali yari, Lisa J. Cohen, Michael R. Crusoe, Tim Head, Luiz Irber, Shannon EK Joslin, N. B. Kingsley, Kevin D. Murray, Russell Neches, Camille Scott, Ryan Shean (+3 others)
2017 Journal of Open Source Software  
The khmer software is a set of command-line tools built around a Python library designed for analysis of large DNA sequence collections.  ...  Pell et al. 2012 Release version 2.1 of the khmer software includes several new features that extend its utility to a wider set of sequence processing and analysis problems.  ... 
doi:10.21105/joss.00272 fatcat:dvsn2kh7rjgf7ejmar4doczwle

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Isabelle Lesur, Grégoire Le Provost, Pascal Bento, Corinne Da Silva, Jean-Charles Leplé, Florent Murat, Saneyoshi Ueno, Jerôme Bartholomé, Céline Lalanne, François Ehrenmann, Céline Noirot, Christian Burban (+15 others)
2015 BMC Genomics  
for oak.  ...  This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.  ...  Hubert for sequencing the putative full-length cDNA clones at the Genome & Transcriptome Facility of Bordeaux.  ... 
doi:10.1186/s12864-015-1331-9 pmid:25765701 pmcid:PMC4350297 fatcat:xy4by7jpw5banjhierqsnslxjm

Genomic resources for a unique, low-virulence Babesia taxon from China

Guiquan Guan, Pasi K. Korhonen, Neil D. Young, Anson V. Koehler, Tao Wang, Youquan Li, Zhijie Liu, Jianxun Luo, Hong Yin, Robin B. Gasser
2016 Parasites & Vectors  
Results: We sequenced and annotated the 8.4 Mb nuclear draft genome of Bx and compared it with those of B. bovis and B. bigemina by synteny analysis; we also investigated the genetic relationship of Bx  ...  with selected Babesia species and related apicomplexans for which genomic datasets are available, and explored the VESA complement in Bx.  ...  Acknowledgements We thank BGI-Shenzhen for sequencing service.  ... 
doi:10.1186/s13071-016-1846-1 pmid:27784333 pmcid:PMC5081931 fatcat:3zbsvgfxcvhbdidsu4ovhsaige

Planctomycetes attached to algal surfaces: Insight into their genomes

Mafalda Faria, Nicola Bordin, Jana Kizina, Jens Harder, Damien Devos, Olga M. Lage
2018 Genomics  
After, the raw sequences were assembled with SPAdes software, annotated in RAST and in Prokka pipeline.  ...  Nowadays, with the development and support of faster and user-friendly in silico tools, used in genome sequencing analysis it is possible to study microorganisms by looking directly at their genomes, even  ...  This may have happened in the sample preparation for the sequencing step, as it was proved that the colonies were pure in before sending to sequence, by the 16S rRNA analysis.  ... 
doi:10.1016/j.ygeno.2017.10.007 pmid:29074368 fatcat:omlm6324mbejxli22mxofcycyq

Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus

Stefano Romano, Antonio Fernàndez-Guerra, F. Jerry Reen, Frank O. Glöckner, Susan P. Crowley, Orla O'Sullivan, Paul D. Cotter, Claire Adams, Alan D. W. Dobson, Fergal O'Gara
2016 Frontiers in Microbiology  
After the quality assessment, the resulting reads were digitally normalized by the khmer software package (Brown et al., 2012) .  ...  Reads were dynamically trimmed and filtered by length using the lowest median value of each paired read by the SolexaQA software suite release 2.0 (Cox et al., 2010) .  ... 
doi:10.3389/fmicb.2016.00387 pmid:27065959 pmcid:PMC4811931 fatcat:2vcqxbmpzra25odwg5fwgnwiqe

Abstracts for the Human Genetics Society of Australasia Virtual Conference 24-25 November 2020

2021 Twin Research and Human Genetics  
Genomic technologies are showing great promise in neonatal and pediatric acute care, particularly as ultra-rapid genomic sequencing (rGS) can now facilitate test results within days for critically unwell  ...  Audio-recorded interviews were transcribed, and data analyzed using reflexive thematic analysis.  ...  Simultaneous sequence and copy number variant analysis combined with customized analysis for difficult to sequence regions in specific genes such as NCF1 improves the diagnostic yield in patients suspected  ... 
doi:10.1017/thg.2021.9 pmid:33900159 fatcat:k62y53jnf5fyvh44d37dq4cfwu