scholarly journals MapCaller – An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced data

2019 ◽  
Author(s):  
Hsin-Nan Lin ◽  
Wen-Lian Hsu
Keyword(s):  
Variant Calling ◽  
Critical Factor ◽  
Personal Genome ◽  
Analysis Tool ◽  
Single Nucleotide Variants ◽  
Read Mapping ◽  
Short Read ◽  
Sequencing Errors ◽  
Short Read Mapping ◽  
Next Generation Sequencing Ngs

AbstractWith the advance of next-generation sequencing (NGS) technologies, more and more medical and biological researches adopt NGS technologies to characterize the genetic variations between individuals. The identification of personal genome variants using NGS technology is a critical factor for the success of clinical genomics studies. It requires an accurate and consistent analysis procedure to distinguish functional or disease-associated variants from false discoveries due to sequencing errors or misalignments. In this study, we integrate the algorithms for read mapping and variant calling to develop an efficient and versatile NGS analysis tool, called MapCaller. It not only maps every short read onto a reference genome, but it also detects single nucleotide variants, indels, inversions and translocations at the same time. We evaluate the performance of MapCaller with existing variant calling pipelines using three simulated datasets and four real datasets. The result shows that MapCaller can identify variants accurately. Moreover, MapCaller runs much faster than existing methods. It is available at https://github.com/hsinnan75/MapCaller.

scholarly journals Whisper 2: indel-sensitive short read mapping

2019 ◽  
Author(s):  
Sebastian Deorowicz ◽  
Adam Gudyś
Keyword(s):  
Web Site ◽  
Variant Calling ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Read Mapping ◽  
Short Read ◽  
Short Read Mapping ◽  
Link Type ◽  
Mapping Software

AbstractSummaryWhisper 2 is a short-read-mapping software providing superior quality of indel variant calling. Its running times place it among the fastest existing tools.Availability and Implementationhttps://github.com/refresh-bio/[email protected] informationSupplementary data are available at publisher’s Web site.

scholarly journals SEAL: a distributed short read mapping and duplicate removal tool

2011 ◽  
Vol 27 (15) ◽  
pp. 2159-2160 ◽  
Author(s):  
L. Pireddu ◽  
S. Leo ◽  
G. Zanetti
Keyword(s):  
Read Mapping ◽  
Short Read ◽  
Short Read Mapping

scholarly journals Short Read Mapping: An Algorithmic Tour

2017 ◽  
Vol 105 (3) ◽  
pp. 436-458 ◽  
Author(s):  
Stefan Canzar ◽  
Steven L. Salzberg
Keyword(s):  
Read Mapping ◽  
Short Read ◽  
Short Read Mapping

scholarly journals MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e90581 ◽  
Author(s):  
Wan-Ping Lee ◽  
Michael P. Stromberg ◽  
Alistair Ward ◽  
Chip Stewart ◽  
Erik P. Garrison ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Read Mapping ◽  
Short Read ◽  
Short Read Mapping ◽  
Generation Sequencing

scholarly journals An Efficient GPUAccelerated Implementation of Genomic Short Read Mapping with BWAMEM

2017 ◽  
Vol 44 (4) ◽  
pp. 38-43 ◽  
Author(s):  
Ernst Joachim Houtgast ◽  
VladMihai Sima ◽  
Koen Bertels ◽  
Zaid AlArs
Keyword(s):  
Read Mapping ◽  
Short Read ◽  
Short Read Mapping

scholarly journals Target variant detection in leukemia using unaligned RNA-Seq reads

2018 ◽  
Author(s):  
Eric Olivier Audemard ◽  
Patrick Gendron ◽  
Vincent-Philippe Lavallée ◽  
Josée Hébert ◽  
Guy Sauvageau ◽  
...  
Keyword(s):  
Variant Calling ◽  
The Cancer Genome Atlas ◽  
Rna Seq ◽  
Read Mapping ◽  
Targeted Mutation ◽  
Cancer Genome Atlas ◽  
Computationally Intensive ◽  
And Performance ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data

AbstractMutations identified in each Acute Myeloid Leukemia (AML) patients are useful for prognosis and to select targeted therapies. Detection of such mutations by the analysis of Next-Generation Sequencing (NGS) data requires a computationally intensive read mapping step and application of several variant calling methods. Targeted mutation identification drastically shifts the usual tradeoff between accuracy and performance by concentrating all computations over a small portion of sequence space. Here, we present km, an efficient approach leveraging k-mer decomposition of reads to identify targeted mutations. Our approach is versatile, as it can detect single-base mutations, several types of insertions and deletions, as well as fusions. We used two independent AML cohorts (The Cancer Genome Atlas and Leucegene), to show that mutation detection bykmis fast, accurate and mainly limited by sequencing depth. Therefore,kmallows to establish fast diagnostics from NGS data, and could be suitable for clinical applications.

scholarly journals Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks

2021 ◽  
Author(s):  
Kishwar Shafin ◽  
Trevor Pesout ◽  
Pi-Chuan Chang ◽  
Maria Nattestad ◽  
Alexey Kolesnikov ◽  
...  
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Variant Calling ◽  
High Accuracy ◽  
Superior Performance ◽  
Read Length ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Short Read ◽  
Long Read

Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read based phasing. Third-generation nanopore sequence data has demonstrated a long read length, but current interpretation methods for its novel pore-based signal have unique error profiles, making accurate analysis challenging. Here, we introduce a haplotype-aware variant calling pipeline PEPPER-Margin-DeepVariant that produces state-of-the-art variant calling results with nanopore data. We show that our nanopore-based method outperforms the short-read-based single nucleotide variant identification method at the whole genome-scale and produces high-quality single nucleotide variants in segmental duplications and low-mappability regions where short-read based genotyping fails. We show that our pipeline can provide highly-contiguous phase blocks across the genome with nanopore reads, contiguously spanning between 85% to 92% of annotated genes across six samples. We also extend PEPPER-Margin-DeepVariant to PacBio HiFi data, providing an efficient solution with superior performance than the current WhatsHap-DeepVariant standard. Finally, we demonstrate de novo assembly polishing methods that use nanopore and PacBio HiFi reads to produce diploid assemblies with high accuracy (Q35+ nanopore-polished and Q40+ PacBio-HiFi-polished).

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