https://retrovirology.biomedcentral.com/articles/10.1186/s12977-015-0232-y
Classification and characterization of human endogenous retroviruses; mosaic forms are common

rescript 验证
conda create -y -n rescript

conda activate rescript

conda install -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.5/tested/ -c defaults qiime2 q2cli q2templates q2-types q2-longitudinal q2-feature-classifier 'q2-types-genomics>2023.2' "pandas>=0.25.3" xmltodict ncbi-datasets-pylib

pip install git+https://ghproxy.com//https://github.com/bokulich-lab/RESCRIPt.git

创建COI库
qiime rescript get-ncbi-data --p-query '(cytochrome c oxidase subunit 1[Title] OR cytochrome c oxidase subunit I[Title] OR cytochrome oxidase subunit 1[Title] OR cytochrome oxidase subunit I[Title] OR COX1[Title] OR CO1[Title] OR COI[Title]) AND BARCODE[KYWD])' --verbose --output-dir NCBIdata_BOLDonly2 --o-sequences coi_genbank.qza --o-taxonomy coi_tax.qza

创建16s库

https://drive5.com/usearch/manual/amplification_bias.html
Abundance and amplification bias in amplicon sequencing
序列的丰度和物种的实际丰度 可能偏差比较大

eDNA需要部署的流程和数据库：
1.denoise+blast物种注释
2.denoise+bayes物种注释
3.nextflow 全流程
3.denoise+rdp物种注释（这个不需要 classify-sklearn和RDP类似）
4.训练分类数据库:makeblastdb、qiime2_train
5.BOLD数据库、NT数据库、mitofish、silva、unite
6.qiime2的全流程
7.交互式分析工具、blast server
8.nextflow hifi 全长

https://www.mdpi.com/1422-0067/23/17/9834/htm
Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics
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appnote_miseq_16S.pdf
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e8101c8a-cb61-42c6-85c9-0b380f3e71c9-image.png

https://github.com/B-UMMI/INNUca
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https://www.intechopen.com/chapters/75997
Entropy Based Biological Sequence Study

https://www.frontiersin.org/articles/10.3389/fgene.2021.620009/full
Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing
对血液感染的肺炎克雷伯菌进行的检测 分析了物种及其耐药性和毒力
Albacore v2.2.6
Porechop v0.2.3
quality control was run through Pauvre v0.1.86
filtered using NanoFilt v2.2.0
Canu v1.6 and nanopolish v0.10.16 were used for nanopore long-read-only assembly and polishing
Unicycler v0.4.5 was also used for hybrid assembly of Illumina reads and nanopore reads
Species identification was performed by Kraken Software v2.0.8-beta 这个文献用Kraken鉴定了nanopore物种
CARD database through RGI v4.2.2 (Resistance Gene Identifier)
Real-time analyses were performed by aligning MinION fastq reads to CARD database v3.0.0 through blastn (blast+, v2.2.28), seeking results with identity ≥80%, hit length ≥100 bp, and gene coverage ≥70%.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04089-5
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