LMAS: evaluating metagenomic short de novo assembly methods through defined communities

Critical Assessment of Metagenome Interpretation: the second round of challenges

(2022) Fernando Meyer et al.   NATURE METHODS

LMAS: evaluating metagenomic short de novo assembly methods through defined communities

(2022) Catarina Inês Mendes et al.   GigaScience

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit

(2021) Fernando Meyer et al.   Nature Protocols

GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations

(2020) Nancy Manchanda et al.   BMC GENOMICS

BlobToolKit - Interactive Quality Assessment of Genome Assemblies

(2020) Richard Challis et al.   G3-Genes Genomes Genetics

Developing standards for the microbiome field

(2020) Gregory C. A. Amos et al.   Microbiome

CAMISIM: simulating metagenomes and microbial communities

(2019) Adrian Fritz et al.   Microbiome

New approaches for metagenome assembly with short reads

(2019) Martin Ayling et al.   BRIEFINGS IN BIOINFORMATICS

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

(2019) Samuel M Nicholls et al.   GigaScience

Scalable Genome Assembly through Parallel de Bruijn Graph Construction for Multiple k-mers

(2019) Kanak Mahadik et al.   Scientific Reports

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

(2019) Volkan Sevim et al.   Scientific Data

Simulating Illumina Metagenomic Data with InSilicoSeq

(2018) Hadrien Gourlé et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens

(2018) Natacha Couto et al.   Scientific Reports

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

(2017) Shaun D. Jackman et al.   GENOME RESEARCH

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

(2013) Rayan Chikhi et al.   Algorithms for Molecular Biology

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

(2012) H. Teeling 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

Genome assembly quality: Assessment and improvement using the neutral indel model

(2010) S. Meader et al.   GENOME RESEARCH