MUMmer4: A fast and versatile genome alignment system

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

Sequence of the Sugar Pine Megagenome

(2016) Kristian A. Stevens et al.   GENETICS

No evidence for extensive horizontal gene transfer in the genome of the tardigradeHypsibius dujardini

(2016) Georgios Koutsovoulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence of the Sugar Pine Megagenome

(2016) Kristian A. Stevens et al.   GENETICS

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

(2015) Thomas C. Boothby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PBSIM: PacBio reads simulator—toward accurate genome assembly

(2012) Yukiteru Ono et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

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