[A review on the bioinformatics pipelines for metagenomic research].
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Summary
There are significant differences between the corresponding bioinformatics tools for these data; accordingly, the computational pipelines separately for these two types of data are reviewed.
- Type
- review
- Published
- 2013-01-31
- Cited by
- 9
- References
- 28
- Access
- Open access
- OpenAlex
- https://openalex.org/W19711442
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:41544252
Keywords
Metagenomics, Computational biology, Shotgun sequencing, Biology, Genomics
References
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- Assembly Algorithms for Next-Generation Sequencing Data
- Ab initio gene finding in Drosophila genomic DNA.
- A hidden Markov model that finds genes in E. coli DNA.
- Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea
- InterProScan - an integration platform for the signature-recognition methods in InterPro
- GENMARK: Parallel Gene Recognition for Both DNA Strands
- QIIME allows analysis of high-throughput community sequencing data
- MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes
- Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products.
- SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
- Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
- The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
- An Eulerian path approach to DNA fragment assembly
- SOAP: short oligonucleotide alignment program
- Integrating genomic homology into gene structure prediction
- ARACHNE: a whole-genome shotgun assembler.
- The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
- ARB: a software environment for sequence data.
- KEGG: Kyoto Encyclopedia of Genes and Genomes
Cited by
- Metagenomic sequencing reveals altered metabolic pathways in the oral microbiota of sailors during a long sea voyage
- The Molecular Heterogeneity of Natural Cordyceps sinensis with Multiple Ophiocordyceps sinensis Fungi Challenges the Anamorph-Teleomorph Connection Hypotheses
- Suitability and advantages of abundance-weighted algorithms for the holistic comparison of sample systems
- Dynamic Alterations in Salivary Microbiota Related to Dental Caries and Age in Preschool Children With Deciduous Dentition: A 2-Year Follow-Up Study
- Functional Metagenomic Technologies for the Discovery of Novel Enzymes for Biomass Degradation and Biofuel Production
- High-throughput sequencing identifies salivary microbiota in Chinese caries-free preschool children with primary dentition
- The Oral Microbiome and Salivary Proteins Influence Caries in Preschool Children
- Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions
- Sea cucumbers as bioindicators of pollution and sea cucumber microbiomes as markers of environmental stress: A review
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