The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data

A McKenna, M Hanna, E Banks, A Sivachenko… - Genome …, 2010 - genome.cshlp.org
Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are
already revolutionizing our understanding of genetic variation among individuals. However …

[HTML][HTML] Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms

KR Franke, EL Crowgey - Genomics & informatics, 2020 - ncbi.nlm.nih.gov
Advancements in next generation sequencing (NGS) technologies have significantly
increased the translational use of genomics data in the medical field as well as the demand …

Halvade: scalable sequence analysis with MapReduce

D Decap, J Reumers, C Herzeel, P Costanza… - …, 2015 - academic.oup.com
Motivation: Post-sequencing DNA analysis typically consists of read mapping followed by
variant calling. Especially for whole genome sequencing, this computational step is very …

[HTML][HTML] QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation

P Wagle, M Nikolić, P Frommolt - BMC genomics, 2015 - Springer
Abstract Background Next-Generation Sequencing (NGS) has emerged as a widely used
tool in molecular biology. While time and cost for the sequencing itself are decreasing, the …

GenPipes: an open-source framework for distributed and scalable genomic analyses

M Bourgey, R Dali, R Eveleigh, KC Chen… - …, 2019 - academic.oup.com
Background With the decreasing cost of sequencing and the rapid developments in
genomics technologies and protocols, the need for validated bioinformatics software that …

SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision

MS Wiewiórka, A Messina, A Pacholewska… - …, 2014 - academic.oup.com
Many time-consuming analyses of next-generation sequencing data can be addressed with
modern cloud computing. The Apache Hadoop-based solutions have become popular in …

Savant: genome browser for high-throughput sequencing data

M Fiume, V Williams, A Brook, M Brudno - Bioinformatics, 2010 - academic.oup.com
Motivation: The advent of high-throughput sequencing (HTS) technologies has made it
affordable to sequence many individuals' genomes. Simultaneously the computational …

Twelve years of SAMtools and BCFtools

P Danecek, JK Bonfield, J Liddle, J Marshall… - …, 2021 - academic.oup.com
Abstract Background SAMtools and BCFtools are widely used programs for processing and
analysing high-throughput sequencing data. They include tools for file format conversion …

Experiences building Globus Genomics: a next‐generation sequencing analysis service using Galaxy, Globus, and Amazon Web Services

RK Madduri, D Sulakhe, L Lacinski… - Concurrency and …, 2014 - Wiley Online Library
SUMMARY We describe Globus Genomics, a system that we have developed for rapid
analysis of large quantities of next‐generation sequencing genomic data. This system …

[HTML][HTML] DolphinNext: a distributed data processing platform for high throughput genomics

O Yukselen, O Turkyilmaz, AR Ozturk, M Garber… - BMC genomics, 2020 - Springer
Background The emergence of high throughput technologies that produce vast amounts of
genomic data, such as next-generation sequencing (NGS) is transforming biological …