宏基因分析流程
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https://github.com/sunbeam-labs/sunbeam
A robust, extensible metagenomics pipeline -
https://anvio.org/
An open-source, community-driven analysis and visualization platform for microbial 'omics. -
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http://ccb.jhu.edu/people/salzberg/docs/Breitwieser-etal-2017-Metagenomics-review-reprint.pdf
A review of methods and databases for metagenomic
classification and assembly
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https://www.sciencedirect.com/science/article/pii/S0092867419307755#bib6
Benchmarking Metagenomics Tools for Taxonomic Classification -
The obvious disadvantage of protein-level sequence classification is the inability to classify reads originating from non-protein-coding genomic regions. Especially when the genomes of the sequenced microbial strains are also contained in the reference database, Kaiju would be less sensitive than nucleotide-level classifiers, which can assess the entire genome, as seen in the HiSeq and MiSeq data sets. However, due to the high density of protein-coding genes in microbial genomes, the probability of overlap between individual sequencing reads and protein-coding genes increases substantially with increasing read lengths. Furthermore, when using paired-end sequencing, the chance of one mate overlapping with a protein-coding gene is higher than for single-end sequencing, which was also shown in our benchmark where longer and paired-end reads had higher sensitivity compared with shorter single-end reads.
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