Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Fast and accurate genomic analyses using genome graphs

(2019) Goran Rakocevic et al.   NATURE GENETICS

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

(2016) Michael A. Eberle et al.   GENOME RESEARCH

Excess of rare, inherited truncating mutations in autism

(2015) Niklas Krumm et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Indexing Graphs for Path Queries with Applications in Genome Research

(2014) Jouni Siren et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The IPD and IMGT/HLA database: allele variant databases

(2014) James Robinson et al.   NUCLEIC ACIDS RESEARCH

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

(2012) Stephan J. Sanders et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

dbVar and DGVa: public archives for genomic structural variation

(2012) Ilkka Lappalainen et al.   NUCLEIC ACIDS RESEARCH

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Next-generation sequencing for HLA typing of class I loci

(2011) Rachel L Erlich et al.   BMC GENOMICS

Expanding the CODIS core loci in the United States

(2011) Douglas R. Hares   Forensic Science International-Genetics

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. 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

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH