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
More filters
Posted Content
Technology dictates algorithms: Recent developments in read alignment
Mohammed Alser,Jeremy Rotman,Kodi Taraszka,Huwenbo Shi,Pelin Icer Baykal,Harry Taegyun Yang,Victor Xue,Sergey Knyazev,Benjamin D. Singer,Brunilda Balliu,David Koslicki,Pavel Skums,Alexander Zelikovsky,Can Alkan,Onur Mutlu,Serghei Mangul +15 more
TL;DR: This review provides a survey of algorithmic foundations and methodologies across 107 alignment methods published between 1988 and 2020, for both short and long reads, and separately discusses how longer read lengths produce unique advantages and limitations to read alignment techniques.
Journal ArticleDOI
Natural RNA Polymerase Aptamers Regulate Transcription in E. coli
Nadezda Sedlyarova,Philipp Rescheneder,Andrés Magán,Niko Popitsch,Natascha Rziha,Ivana Bilusic,Vitaly Epshtein,Bob Zimmermann,Meghan Lybecker,Vitaly Sedlyarov,Renée Schroeder,Evgeny Nudler +11 more
TL;DR: This work deep sequenced an E. coli genomic library enriched for RNAP-binding RNAs and characterized a subset of inhibitory RAPs (iRAPs) that promote Rho-dependent transcription termination, finding a broad class of cis-acting RNA signals that globally control bacterial transcription.
Journal ArticleDOI
lra: A long read aligner for sequences and contigs.
Jingwen Ren,Mark Chaisson +1 more
TL;DR: Chaisson et al. as mentioned in this paper used sparse dynamic programming (SDP) with a concave-cost gap penalty to align long-read sequences from PacBio and Oxford Nanopore (ONT) instruments as well as de novo assembly contigs.
Journal ArticleDOI
A transposable element insertion is associated with an alternative life history strategy.
Alyssa Woronik,Kalle Tunström,Michael Perry,Ramprasad Neethiraj,Constantí Stefanescu,Maria de la Paz Celorio-Mancera,Oskar Brattström,Jason Hill,Jason Hill,Philipp Lehmann,Reijo Käkelä,Christopher W. Wheat +11 more
TL;DR: A transposable element insertion is associated with the switch between alternative life history strategies, central to life history theory and evolutionary biology, and characterize one such mechanism for a female-limited ALHS.
Journal ArticleDOI
De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia galeata.
Ann Kathrin Huylmans,Ann Kathrin Huylmans,Alberto López Ezquerra,John Parsch,Mathilde Cordellier,Mathilde Cordellier +5 more
TL;DR: A de novo transcriptome assembly of over 32,000 D. galeata genes is presented and it is found that only a low percentage of genes shows sex-biased expression and that there are many more female- biased gene (FBG) than male-biased gene (MBG) and FBGs tend to be more conserved between species than MBGs in both sequence and expression.
References
More filters
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Journal ArticleDOI
Genotype and SNP calling from next-generation sequencing data
TL;DR: Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data.
Journal ArticleDOI
Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.
Gerton Lunter,Martin Goodson +1 more
TL;DR: A read mapper, Stampy, which uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation, which results in a higher useable sequence yield and improved accuracy compared to that of existing software.
Journal ArticleDOI
Tools for mapping high-throughput sequencing data
TL;DR: This survey focuses on classifying mappers through a wide number of characteristics to allow practitioners to compare the mappers more easily and find those that are most suitable for their specific problem.