ArticlePLoS computational biology2016
NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
36 citing papers in PubMed, 82 citations in OpenAlex.
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- Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables.Scientific reports · 2023Article
- Impacts of biostimulation and bioaugmentation on woodchip bioreactor microbiomes.Microbiology spectrum · 2023Article
- Structure and Functional Properties of Bacterial Communities in Surface Sediments of the Recently Declared Nutrient-Saturated Lake Villarrica in Southern Chile.Microbial ecology · 2023Article
- Effect of water management on microbial diversity and composition in an Italian rice field system.FEMS microbiology ecology · 2022Article
- Depletion of the Microbiota Has a Modest but Important Impact on the Fungal Burden of the Heart and Lungs during Early SystemicMicroorganisms · 2022Article
- Gut microbiota response to antibiotics is personalized and depends on baseline microbiota.Microbiome · 2021Article
- Erosion reduces soil microbial diversity, network complexity and multifunctionality.The ISME journal · 2021Article
- An Assessment of theMicroorganisms · 2021Article
- Composition and predicted functions of the bacterial community in spouting pool sediments from the El Tatio Geyser field in Chile.Archives of microbiology · 2021Article
- A murine model to study the gut bacteria parameters during complex antibiotics like cefotaxime and ceftriaxone treatment.Computational and structural biotechnology journal · 2021Article
- An ambient temperature collection and stabilization strategy for canine microbiota studies.Scientific reports · 2020Article
- Wild primate microbiomes prevent weight gain in germ-free mice.Animal microbiome · 2020Article
- Interactions between the gut microbiome and host gene regulation in cystic fibrosis.Genome medicine · 2020Article
- Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing Data.Frontiers in genetics · 2020Article
- Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan.International journal of environmental research and public health · 2019Article
- Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota.Genome biology · 2019Article
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Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
The explosion of bioinformatics technologies in the form of next generation sequencing (NGS) has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene sequencing studies, which have mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA for short), a fast and highly accurate novel method enabling reference-based marker gene matching (picking Operational Taxonomic Units, or OTUs). NINJA takes advantage of the Burrows-Wheeler (BW) alignment using an artificial reference chromosome composed of concatenated reference sequences, the "concatesome," as the BW input. Other features include automatic support for paired-end reads with arbitrary insert sizes. NINJA is also free and open source and implements several pre-filtering methods that elicit substantial speedup when coupled with existing tools. We applied NINJA to several published microbiome studies, obtaining accuracy similar to or better than previous reference-based OTU-picking methods while achieving an order of magnitude or more speedup and using a fraction of the memory footprint. NINJA is a complete pipeline that takes a FASTA-formatted input file and outputs a QIIME-formatted taxonomy-annotated BIOM file for an entire MiSeq run of human gut microbiome 16S genes in under 10 minutes on a dual-core laptop.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.