NextGenMap: Fast and accurate read mapping in highly polymorphic genomes
TLDR
NextGenMap is reported, a fast and accurate read mapper, which aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large, i.e. highly polymorphic genome.Abstract:
Summary: When choosing a read mapper, one faces the trade off between speed and the ability to map reads in highly polymorphic regions. Here, we report NextGenMap, a fast and accurate read mapper, which reduces this dilemma. NextGenMap aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large, i.e. highly polymorphic genome. At the same time, NextGenMap outperforms current mapping methods with respect to runtime and to the number of correctly mapped reads. NextGenMap efficiently uses the available hardware by exploiting multi-core CPUs as well as graphic cards (GPUs), if available. In addition, NextGenMap handles automatically any read data independent of read length and sequencing technology. Availability: NextGenMap source code and documentation are available at: http://cibiv.github.io/NextGenMap/ Contact: fritz.sedlazeck@univie.ac.at Supplementary information: Supplementary data are available at Bioinformatics online.read more
Citations
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Journal ArticleDOI
Accurate detection of complex structural variations using single-molecule sequencing.
Fritz J. Sedlazeck,Philipp Rescheneder,Moritz Smolka,Han Fang,Maria Nattestad,Arndt von Haeseler,Arndt von Haeseler,Michael C. Schatz,Michael C. Schatz +8 more
TL;DR: NGMLR and Sniffles perform highly accurate alignment and structural variation detection from long-read sequencing data and can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings.
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Tumor Cell-Intrinsic Factors Underlie Heterogeneity of Immune Cell Infiltration and Response to Immunotherapy
Jinyang Li,Katelyn T. Byrne,Fangxue Yan,Taiji Yamazoe,Zeyu Chen,Timour Baslan,Lee P. Richman,Jeffrey H. Lin,Yu H. Sun,Andrew J. Rech,David Balli,Ceire A. Hay,Yogev Sela,Allyson J. Merrell,Shannon M. Liudahl,Naomi Gordon,Robert J. Norgard,Salina Yuan,Sixiang Yu,Timothy Chao,Shuai Ye,T.S. Karin Eisinger-Mathason,Robert B. Faryabi,John W. Tobias,Scott W. Lowe,Scott W. Lowe,Lisa M. Coussens,E. John Wherry,Robert H. Vonderheide,Ben Z. Stanger +29 more
TL;DR: A library of congenic tumor cell clones from an autochthonous mouse model of pancreatic adenocarcinoma is established, identifying heterogeneous and multifactorial pathways regulating tumor‐cell‐intrinsic mechanisms that dictate the immune microenvironment and thereby responses to immunotherapy.
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DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
Manu J. Dubin,Pei Zhang,Dazhe Meng,Marie Stanislas Remigereau,Edward J. Osborne,Francesco Paolo Casale,Philipp Drewe,André Kahles,Géraldine Jean,Bjarni J. Vilhjálmsson,Joanna Jagoda,Selen Irez,Viktor Voronin,Qiang Song,Quan Long,Gunnar Rätsch,Oliver Stegle,Richard M. Clark,Magnus Nordborg +18 more
TL;DR: Investigation of DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures finds that accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected.
Journal ArticleDOI
Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.
Daniel C. Jeffares,Clare Jolly,Mimoza Hoti,Doug Speed,Liam P. Shaw,Charalampos Rallis,Charalampos Rallis,Francois Balloux,Christophe Dessimoz,Jürg Bähler,Fritz J. Sedlazeck +10 more
TL;DR: It is shown that copy number variants (CNVs) show a variety of genetic signals consistent with rapid turnover and make substantial contributions to quantitative traits, most notably intracellular amino acid concentrations, growth under stress and sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation.
Journal ArticleDOI
Genome sequence of mungbean and insights into evolution within Vigna species
Yang Jae Kang,Sue K. Kim,Moon Young Kim,Puji Lestari,Kil Hyun Kim,Bo-Keun Ha,Tae-Hwan Jun,Won Joo Hwang,Taeyoung Lee,Jayern Lee,Sangrea Shim,Minyoung Yoon,Young Eun Jang,Kwang Soo Han,Puntaree Taeprayoon,Na Rae Yoon,Prakit Somta,Patcharin Tanya,Kwang Soo Kim,Jae-Gyun Gwag,Jung-Kyung Moon,Yeong-Ho Lee,Beom-Seok Park,Aureliano Bombarely,Jeff J. Doyle,Scott A. Jackson,Roland Schafleitner,Peerasak Srinives,Rajeev K. Varshney,Suk-Ha Lee +29 more
TL;DR: A draft genome sequence of mungbean is constructed to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species.
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