sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data

NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data

(2018) Li Fang et al.   BMC BIOINFORMATICS

The landscape of genomic alterations across childhood cancers

(2018) Susanne N. Gröbner et al.   NATURE

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours

(2018) Xiaotu Ma et al.   NATURE

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

(2017) Daniel L. Cameron et al.   GENOME RESEARCH

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

svclassify: a method to establish benchmark structural variant calls

(2016) Hemang Parikh et al.   BMC GENOMICS

A review of bioinformatic pipeline frameworks

(2016) Jeremy Leipzig   BRIEFINGS IN BIOINFORMATICS

A Medium-Scale Distributed System for Computer Science Research: Infrastructure for the Long Term

(2016) Henri Bal et al.   COMPUTER

Extensive sequencing of seven human genomes to characterize benchmark reference materials

(2016) Justin M. Zook et al.   Scientific Data

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing

(2015) Marghoob Mohiyuddin et al.   BIOINFORMATICS

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Assessing structural variation in a personal genome—towards a human reference diploid genome

(2015) Adam C English et al.   BMC GENOMICS

Making the difference: integrating structural variation detection tools

(2014) Ke Lin et al.   BRIEFINGS IN BIOINFORMATICS

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Exploring the Genomes of Cancer Cells: Progress and Promise

(2011) M. R. Stratton   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS