Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

Effect of lossy compression of quality scores on variant calling

(2016) Idoia Ochoa et al.   BRIEFINGS IN BIOINFORMATICS

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Fast search of thousands of short-read sequencing experiments

(2016) Brad Solomon et al.   NATURE BIOTECHNOLOGY

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Extensive sequencing of seven human genomes to characterize benchmark reference materials

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

BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The UK10K project identifies rare variants in health and disease

(2015)   NATURE

Quality score compression improves genotyping accuracy

(2015) Y William Yu et al.   NATURE BIOTECHNOLOGY

Genomic evidence for the Pleistocene and recent population history of Native Americans

(2015) M. Raghavan et al.   SCIENCE

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Extending reference assembly models

(2015) Deanna M Church et al.   GENOME BIOLOGY

BEETL-fastq: a searchable compressed archive for DNA reads

(2014) L. Janin et al.   BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Large scale comparison of non-human sequences in human sequencing data

(2014) Hongseok Tae et al.   GENOMICS

Whole-genome sequence variation, population structure and demographic history of the Dutch population

(2014) Laurent C Francioli et al.   NATURE GENETICS

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data

(2014) Richard W. Lusk   PLoS One

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Molecular genetic testing and the future of clinical genomics

(2013) Sara Huston Katsanis et al.   NATURE REVIEWS GENETICS

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

(2012) A. J. Cox et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Efficient storage of high throughput DNA sequencing data using reference-based compression

(2011) M. Hsi-Yang Fritz et al.   GENOME RESEARCH

Current prevalence of HTLV-1 in Japan as determined by screening of blood donors

(2011) Masahiro Satake et al.   JOURNAL OF MEDICAL VIROLOGY

Microbial Metagenomics: Beyond the Genome

(2010) Jack A. Gilbert et al.   Annual Review of Marine Science

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY