ngs LCA —A toolkit for fast and flexible lowest common ancestor inference and taxonomic profiling of metagenomic data

Environmental genomics of Late Pleistocene black bears and giant short-faced bears

(2021) Mikkel Winther Pedersen et al.   CURRENT BIOLOGY

Metagenomics: A viable tool for reconstructing herbivore diet

(2021) Physilia Y.S. Chua et al.   Molecular Ecology Resources

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments

(2021) Benjamin Vernot et al.   SCIENCE

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index

(2021) Fatemeh Almodaresi et al.   BIOINFORMATICS

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

(2021) Yucheng Wang et al.   NATURE

Comparing whole‐genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures

(2021) Karen L. Bell et al.   Ecology and Evolution

PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea

(2020) Becky Cribdon et al.   Frontiers in Ecology and Evolution

Mutation-Simulator: Fine-grained simulation of random mutations in any genome

(2020) M A Kühl et al.   BIOINFORMATICS

Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples

(2020) Mads Reinholdt Jensen et al.   Molecular Ecology Resources

Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA

(2019) Krista M. Ruppert et al.   Global Ecology and Conservation

A review on the applications and recent advances in environmental DNA (eDNA) metagenomics

(2019) Deviram Garlapati et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula

(2018) Dominique A. Cowart et al.   Marine Genomics

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Postglacial viability and colonization in North America’s ice-free corridor

(2016) Mikkel W. Pedersen et al.   NATURE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

Genome sequence of a 45,000-year-old modern human from western Siberia

(2014) Qiaomei Fu et al.   NATURE

Wildlife health investigations: needs, challenges and recommendations

(2013) Marie-Pierre Ryser-Degiorgis   BMC Veterinary Research

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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