Results 31 to 40 of about 37,179 (261)

Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection [version 1; referees: 2 approved, 1 approved with reservations]

Wellcome Open Research, 2017
Identifying variants from RNA-seq (transcriptome sequencing) data is a cost-effective and versatile alternative to whole-genome sequencing. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic
Laura Oikkonen, Stefano Lise
doaj   +1 more source

Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

BMC Bioinformatics, 2021
Background Next-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical, data interpretation and management challenges.
Maria Zanti, Kyriaki Michailidou, Maria A. Loizidou, Christina Machattou, Panagiota Pirpa, Kyproula Christodoulou, George M. Spyrou, Kyriacos Kyriacou, Andreas Hadjisavvas   +8 more
doaj   +1 more source

Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy

Frontiers in Genetics, 2019
As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important.
Katherine I. Kendig, Saurabh Baheti, Matthew A. Bockol, Travis M. Drucker, Steven N. Hart, Jacob R. Heldenbrand, Mikel Hernaez, Matthew E. Hudson, Matthew E. Hudson, Michael T. Kalmbach, Eric W. Klee, Nathan R. Mattson, Christian A. Ross, Morgan Taschuk, Eric D. Wieben, Mathieu Wiepert, Derek E. Wildman, Derek E. Wildman, Liudmila S. Mainzer, Liudmila S. Mainzer   +19 more
doaj   +1 more source

elPrep 4: A multithreaded framework for sequence analysis.

PLoS ONE, 2019
We present elPrep 4, a reimplementation from scratch of the elPrep framework for processing sequence alignment map files in the Go programming language.
Charlotte Herzeel, Pascal Costanza, Dries Decap, Jan Fostier, Wilfried Verachtert   +4 more
doaj   +1 more source

HAP1 variants called using GATK used in SGE of BAP1

, 2023
Variants processed through the GATK pipeline from whole genome sequencing of the HAP1-A5 Cas9+ HAP1- clonal line used in SGE of BAP1.
David Adams (10283936)
core   +1 more source

Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection [version 2; referees: 2 approved, 1 approved with reservations]

Wellcome Open Research, 2017
Identifying variants from RNA-seq (transcriptome sequencing) data is a cost-effective and versatile complement to whole-exome (WES) and whole-genome sequencing (WGS) analysis.
Laura Oikkonen, Stefano Lise
doaj   +1 more source

GATK Methods for Bacterial Variant Discovery and Evaluation

, 2020
GATK methods for variant discovery and evaluation in bacteria, resolve inconsistent and diverse results from different research groups, and allow for the sharing of data and analysis globally to control bacterial transmission and antibiotic ...
Bhanu Gandham, Dijk, Lucas Van
openaire   +1 more source

High-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Time. [PDF]

PLoS ONE, 2017
Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome
Tiffany M Jamann, Shilpa Sood, Randall J Wisser, James B Holland   +3 more
doaj   +1 more source

Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data.

PLoS ONE, 2017
Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the ...
Bo-Young Kim, Jung Hoon Park, Hye-Yeong Jo, Soo Kyung Koo, Mi-Hyun Park   +4 more
doaj   +1 more source

Accurate sequence variant genotyping in cattle using variation-aware genome graphs

Genetics Selection Evolution, 2019
Background Genotyping of sequence variants typically involves, as a first step, the alignment of sequencing reads to a linear reference genome. Because a linear reference genome represents only a small fraction of all the DNA sequence variation within a ...
Danang Crysnanto, Christine Wurmser, Hubert Pausch   +2 more
doaj   +1 more source