• MEGAN

  • Referenced in 17 articles [sw33189]
  • MEGAN analysis of metagenomic data. Metagenomics is the study of the genomic content ... program that allows laptop analysis of large metagenomic data sets. In a preprocessing step ... Sargasso Sea data set, a recently published metagenomic data set sampled from a mammoth bone...
  • RAST

  • Referenced in 7 articles [sw17158]
  • metagenomics RAST server — a public resource for the automatic phylogenetic and functional analysis of metagenomes ... Background: Random community genomes (metagenomes) are now commonly used to study microbes in different environments ... years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput ... next-generation sequencing has provided access to metagenomics to a wide range of researchers. Results...
  • SPAdes

  • Referenced in 9 articles [sw17004]
  • cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated ... exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru...
  • Dendroscope

  • Referenced in 12 articles [sw21230]
  • such as arise in expression analysis or metagenomics, for example. It would be desirable...
  • FragGeneScan

  • Referenced in 4 articles [sw17159]
  • next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole ... material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads ... important yet challenging problem in annotating metagenomes, since the assembly of metagenomes is often ... genomes (e.g. Glimmer) and recently developed for metagenomic sequences (e.g. MetaGene) show a significant decrease...
  • GOLD

  • Referenced in 5 articles [sw23027]
  • such as isolate genome, single-cell genome, metagenome, metatranscriptome) and complex Analysis Projects (such ... genome from metagenome, or combined assembly from multiple Sequencing Projects). GOLD provides a seamless interface...
  • MetaSim

  • Referenced in 3 articles [sw23453]
  • MetaSim - A Sequencing Simulator for Genomics and Metagenomics. Background: The new research field of metagenomics ... statistical methods for dealing with complex metagenome data sets. Methodology/Principal Findings: To facilitate the development ... improvement of metagenomic tools and the planning of metagenomic projects, we introduce a sequencing simulator ... reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database...
  • MEGAHIT

  • Referenced in 3 articles [sw23963]
  • single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. MEGAHIT ... novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient ... manner. It finished assembling a soil metagenomics dataset with 252 Gbps...
  • CLARK

  • Referenced in 2 articles [sw23452]
  • CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. Background ... introduce Clark a novel approach to classify metagenomic reads at the species or genus level ... high speed. Extensive experimental results on various metagenomic samples show that the classification accuracy ... classifies, with high accuracy, about 32 million metagenomic short reads per minute. Clark can also...
  • Bambus 2

  • Referenced in 2 articles [sw29700]
  • Bambus 2: scaffolding metagenomes. Motivation: Sequencing projects increasingly target samples from non-clonal sources ... particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities ... some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination ... than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between...
  • TagCleaner

  • Referenced in 2 articles [sw17154]
  • removal of tag sequences from genomic and metagenomic datasets. Background: Sequencing metagenomes that were ... detect and efficiently remove tag sequences from metagenomic datasets. It is easily configurable and provides...
  • Meta-IDBA

  • Referenced in 2 articles [sw17340]
  • read assembler specially designed for de novo metagenomic assembly. One of the most difficult problem ... metagenomic assembly is that similar subspecies of the same species mix together to make...
  • MetaProb

  • Referenced in 2 articles [sw23450]
  • Metagenomic reads binning with spaced seeds. The growing number of sequencing projects in medicine ... algorithm called MetaProb that can accurately cluster metagenomic reads with a precision that is currently...
  • Mash

  • Referenced in 2 articles [sw28785]
  • Mash: fast genome and metagenome distance estimation using MinHash. Mash extends the MinHash dimensionality-reduction ... scalable clustering of hundreds of metagenomic samples by composition. Mash is freely released under...
  • MG-RAST

  • Referenced in 1 article [sw23115]
  • RAST: Metagenomics RAST Server. The metagenomics RAST server is a SEED-based environment that allows ... users to upload metagenomes for automated analyses. The server is built as a modified version ... SEED data and has been adapted for metagenome analysis. The server provides the annotation ... classification of samples, and comparison between multiple metagenomes. The server also computes an initial metabolic...
  • MetaSpark

  • Referenced in 1 article [sw23875]
  • spark-based distributed processing tool to recruit metagenomic reads to reference genomes. With the advent ... bioinformatics tools are challenged by massive raw metagenomic datasets. One of the bottlenecks of metagenomic ... Spark-based tool, called MetaSpark, to recruit metagenomic reads to reference genomes. MetaSpark benefits from ... well with the datasets. Compared with previous metagenomics recruitment tools, MetaSpark recruited significantly more reads...
  • MetaVelvet

  • Referenced in 1 article [sw17337]
  • extension of Velvet assembler to De Novo metagenome assembly from short sequence reads. An important ... step in ‘metagenomics’ analysis is the assembly of multiple genomes from mixed sequence reads ... single-genome assembler for de novo metagenome assembly is that sequences of highly abundant species ... short reads, known as ‘Velvet’, to metagenome assembly, which we called ‘MetaVelvet’, for mixed short...
  • MOCAT

  • Referenced in 1 article [sw23026]
  • MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit. MOCAT is a highly configurable, modular pipeline ... quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several ... predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction ... tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics...
  • EMDUnifrac

  • Referenced in 2 articles [sw17710]
  • profiles resulting from classifying whole genome shotgun metagenomes. The EMDUnifrac source code (written in python...