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

A comparative study of RNA-seq analysis strategies

(2015) J. Janes et al.   BRIEFINGS IN BIOINFORMATICS

Why we need more algal genomes

(2015) Debashish Bhattacharya et al.   JOURNAL OF PHYCOLOGY

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

(2015) Armin Erlacher et al.   Frontiers in Microbiology

Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA inAsclepias(Apocynaceae)

(2015) Kevin Weitemier et al.   PeerJ

Omega: an Overlap-graph de novo Assembler for Metagenomics

(2014) Bahlul Haider et al.   BIOINFORMATICS

Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota)

(2014) Yan-Yan Wang et al.   BMC GENOMICS

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

(2014) Martin Grube et al.   ISME Journal

Bacterial phylogeny structures soil resistomes across habitats

(2014) Kevin J. Forsberg et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

GAGE-B: an evaluation of genome assemblers for bacterial organisms

(2013) Tanja Magoc 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

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke

(2013) Dan G. Bock et al.   NEW PHYTOLOGIST

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

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

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

(2013) Keith R Bradnam et al.   GigaScience

GemSIM: general, error-model based simulator of next-generation sequencing data

(2012) Kerensa E McElroy et al.   BMC GENOMICS

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

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

Exploring symbiont management in lichens

(2012) MARTIN GRUBE 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

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Integrative analysis of environmental sequences using MEGAN4

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

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Insights from the first putative biosynthetic gene cluster for a lichen depside and depsidone

(2011) Daniele Armaleo et al.   MYCOLOGIA

How to apply de Bruijn graphs to genome assembly

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

Bacterial Communities Associated with the Lichen Symbiosis

(2010) Scott T. Bates et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

Desiccation-Tolerance in Lichens: A Review

(2008) Ilse Kranner et al.   BRYOLOGIST

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

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

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One

6-MSAS-like polyketide synthase genes occur in lichenized ascomycetes

(2007) Imke Schmitt et al.