Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Symbiosis-inspired approaches to antibiotic discovery

(2017) Navid Adnani et al.   NATURAL PRODUCT REPORTS

Environment and host identity structure communities of green algal symbionts in lichens

(2017) Francesco Dal Grande et al.   NEW PHYTOLOGIST

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Panmixia and dispersal from the Mediterranean Basin to Macaronesian Islands of a macrolichen species

(2017) David Alors et al.   Scientific Reports

Putative identification of the usnic acid biosynthetic gene cluster by de novo whole-genome sequencing of a lichen-forming fungus

(2016) Mona Abdel-Hameed et al.   Fungal Biology

High Life Expectancy of Bacteria on Lichens

(2016) Tomislav Cernava et al.   MICROBIAL ECOLOGY

From barcodes to genomes: extending the concept of DNA barcoding

(2016) Eric Coissac et al.   MOLECULAR ECOLOGY

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2016) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Basidiomycete yeasts in the cortex of ascomycete macrolichens

(2016) Toby Spribille et al.   SCIENCE

Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches

(2016) Steven D. Leavitt et al.   Scientific Reports

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

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

Understanding Microbial Multi-Species Symbioses

(2016) Ines A. Aschenbrenner et al.   Frontiers in Microbiology

Characterization of Microsatellite Loci in the Lichen-Forming FungusCetraria aculeata(Parmeliaceae, Ascomycota)

(2016) Tetiana Lutsak et al.   Applications in Plant Sciences

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

NxTrim: optimized trimming of Illumina mate pair reads: Table 1.

(2015) Jared O’Connell et al.   BIOINFORMATICS

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

(2015) Michael A. Peabody et al.   BMC BIOINFORMATICS

Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research

(2015) Anna Papadopoulou et al.   MOLECULAR ECOLOGY

Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens

(2015) Bastian Greshake et al.   Molecular Ecology Resources

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

Mycobiont-photobiont interactions of the lichen Cetraria aculeata in high alpine regions of East Africa and South America

(2015) Tetiana Lutsak et al.   SYMBIOSIS

Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L.

(2015) Armin Erlacher et al.   Frontiers in Microbiology

Systems-based approaches to unravel multi-species microbial community functioning

(2015) Florence Abram   Computational and Structural Biotechnology Journal

Omega: an Overlap-graph de novo Assembler for Metagenomics

(2014) Bahlul Haider et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics

(2014) Martin Grube et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family

(2013) Tami R McDonald et al.   BMC GENOMICS

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

(2013) A. Kampa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Twenty-five cultures of lichenizing fungi available for experimental studies on symbiotic systems

(2013) Tami R. McDonald et al.   SYMBIOSIS

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies

(2012) J. Droge et al.   BRIEFINGS IN BIOINFORMATICS

Reference databases for taxonomic assignment in metagenomics

(2012) M. Santamaria et al.   BRIEFINGS IN BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Vertical and horizontal photobiont transmission within populations of a lichen symbiosis

(2012) F. DAL GRANDE et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

Lichen extracts as raw materials in perfumery. Part 1: oakmoss

(2009) Daniel Joulain et al.   FLAVOUR AND FRAGRANCE JOURNAL

Lichen extracts as raw materials in perfumery. Part 2: treemoss

(2009) Daniel Joulain et al.   FLAVOUR AND FRAGRANCE JOURNAL

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH