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编程小6 后端 (6) 2024-04-11 16:23

Hi，大家好，我是编程小6，很荣幸遇见你，我把这些年在开发过程中遇到的问题或想法写出来，今天说一说Github中文镜像_github镜像知乎,希望能够帮助你!!!。
血清型分析网站

Center for Genomic Epidemiology

1.介绍

血清型又称血清蛋白型，指存在于血浆中蛋白质的遗传标记。

血清型是指病毒和细菌中特定不同的亚种。这些微生物一般都由细胞表层的抗原来分类命名的。但是在同一种类的微生物里也会有分支和不同。

血清型的决定是由很多种类的因素而形成的，其中不乏包括病毒性、革兰氏阴性菌表层的脂多糖、外毒素、细菌的质粒和噬菌体等。通过聚合酶链式反应，也可以利用基因特性来分别不同的血清型。

一般来说，血清分型是基于体细胞O抗原 (somatic O antigen)、细胞表面蛋白和构成鞭毛一部分的H抗原或基于荚膜多糖（CPS）K抗原

2.沙门菌血清型预测

H+O，测试使用GCF_000006945.2

2.1 SeqSero，后续版本SeqSero2

SeqSero：https://cge.food.dtu.dk/services/SeqSero/

SeqSero2：SeqSero-Salmonella Serotyping by Whole Genome Sequencing

支持使用原始reads数据或者全基因组组装序列进行分析，

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2.2 MOST血清型预测

英国公共卫生部开发的MOST工具，利用SRST工具分析全基因组测序数据，并结合MLST分型结果，以识别相应的血清型

https://github.com/phe-bioinformatics/MOST

2.3 SalmonellaTypeFinder

丹麦科技大学开发的网页版工具SalmonellaTypeFinder，运行SeqSero预测血清型并应用SRST2确定MLST分型，最终结合两种分型工具的结果预测沙门菌的血清型

Bitbucket

在线网站链接好像失效了

2.4 SISTR

SISTR则是结合cgMLST分型策略预测沙门菌的血清型，其准确率可达94.6%

https://github.com/phac-nml/sistr_cmd#web-application

3.大肠埃希菌血清型预测

大肠埃希菌的菌体抗原(O)、荚膜抗原(K)、鞭毛抗原(H)和菌毛抗原(F)是其血清型鉴定和分型的基础

测试使用GCF_000005845.2

3.1 SerotypeFinder

Joensen等学者创建基于大肠埃希菌全基因组数据预测其血清型分型的在线分析工具SerotypeFinder，该工具基于特定O抗原基因(wzx、wzy、wzm和wzt)和H抗原基因(fliC、flkA、fllA、flmA和flnA)序列的分型方法与传统血清学结果具有高度一致性

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3.2 ClermonTyping

在线工具ClermonTyping可将大肠埃希菌细分为A、B1、B2、C、D、E和F七个主要的亚群(phylogroups)，从而替代传统的多重PCR方法对大肠埃希菌进行亚种分型

http://clermontyping.iame-research.center

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4.肺炎克雷伯菌血清型预测

K+O，测试使用GCF_000240185.1

4.1 Kaptive

Kaptive Web是一种快速鉴别肺炎克雷伯菌K (编码荚膜多糖)和O位点(编码脂多糖O抗原)的在线工具

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4.2 Pathogenwatch

pathogen.watch在线网站也可以做肺炎克雷伯菌的血清型预测，预测操作见：Kleborate：肺炎克雷伯菌分析

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5.鲍曼不动杆菌

2020年最新版本的Kaptive Web增加了对鲍曼不动杆菌荚膜多糖(capsular polysaccharide，KL)和脂寡糖外核心(lipooligosaccharide outer core，OCL)的识别

表格：

Name	Description	Accessibility	Link
chewBBACA	cg/wgMLST schema creation and allele calling using genome assemblies (FASTA)	Web & Standalone	https://chewbbaca.online https://github.com/B-UMMI/chewBBACA
MentaLiST	cg/wgMLST schema creation and allele calling using raw sequencing reads (FASTQ) or genome assemblies (FASTA)	Standalone	https://github.com/WGS-TB/MentaLiST
Genome profiler	cg/wgMLST schema creation and allele calling using genome assemblies (FASTA)	Standalone	http://sourceforge.net/projects/genomeprofiler
In silico typing
SeqSero	Salmonella serotype prediction using raw sequencing reads (FASTQ) or genome assemblies (FASTA)	Web & Standalone	http://denglab.info/SeqSero https://github.com/denglab/SeqSero
SeqSero2	Similar to SeqSero (an updated version)	Web & Standalone	https://github.com/denglab/SeqSero2 http://www.denglab.info/SeqSero2
MOST	Salmonella serotype prediction and MLST allele calling using raw sequencing reads (FASTQ)	Standalone	https://github.com/phe-bioinformatics/MOST
SalmonellaTypeFinder	Salmonella serotype prediction and MLST allele calling using raw sequencing reads (FASTQ)	Web & Standalone	https://bitbucket.org/genomicepidemiology/salmonellatypefinder/src/master/ https://cge.cbs.dtu.dk/services/SalmonellaTypeFinder
SISTR	Salmonella serotype prediction and cgMLST allele calling using genome assemblies (FASTA)	Web & Standalone	https://lfz.corefacility.ca/sistr-app https://github.com/phac-nml/SISTR_cmd
SerotypeFinder	E. coli serotype prediction using raw sequencing reads (FASTQ) or genome assemblies (FASTA)	Web & Standalone	https://cge.cbs.dtu.dk/services/SerotypeFinder
Kaptive	Capsule and lipopolysaccharide serotype prediction for Klebsiella pneumoniae and Acinetobacter baumannii genome assemblies (FASTA)	Web & Standalone	https://kaptive-web.erc.monash.edu/ https://github.com/katholt/Kaptive
ClermonTyping	In silico Escherichia genus strain phylotyping using genome assemblies (FASTA)	Web & Standalone	http://clermontyping.iame-research.center https://github.com/A-BN/ClermonTyping
pMLST	In silico plasmid multilocus sequence typing using genome assemblies (FASTA)	Web & Standalone	https://pubmlst.org/organisms/plasmid-mlst
PlasmidFinder	In silico characterization of plasmid replicons from Enterobacteriaceae using raw sequencing reads (FASTQ) or genome assemblies (FASTA)	Web & Standalone	https://cge.cbs.dtu.dk/services/PlasmidFinder
PLACNETw	A graph-based tool for plasmid reconstruction using raw sequencing reads (FASTQ)	Web & Standalone	https://castillo.dicom.unican.es/upload https://github.com/LuisVielva/PLACNETw
oriTfinder	Identification of bacterial mobile genetic elements using genome assemblies (FASTA) or GenBank files	Web & Standalone	https://bioinfo-mml.sjtu.edu.cn/oriTfinder
Phylogenetic inference
Gubbins	Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using a multi-FASTA alignment file	Standalone	https://github.com/sanger-pathogens/gubbins
RecHMM	Detection of recombinant breakpoints and tree-topology changes in whole-genome sequence alignments using a multi-FASTA alignment file	Standalone	http://biowiki.org/wiki/index.php/Rec_HMM
PhyML	Fast maximum likelihood-based phylogenetic inference using a PHYLIP format alignment file	Web & Standalone	http://www.atgc-montpellier.fr/phyml https://github.com/stephaneguindon/phyml
RAxML	Phylogenetic analyses of large datasets under maximum likelihood using a multi-FASTA alignment file	Standalone	https://github.com/stamatak/standard-RAxML
IQ-TREE	A fast and effective algorithm to infer phylogenetic trees by maximum likelihood using an alignment file in various common formats	Web & Standalone	http://iqtree.cibiv.univie.ac.at http://www.iqtree.org
MrBayes	A variety of phylogenetic and evolutionary models based on Bayesian inference using a NEXUS format alignment file	Standalone	http://nbisweden.github.io/MrBayes
BEAST	A cross-platform program for time-measured Bayesian phylogenetic analysis and phylodynamic data integration using an alignment file in various common formats	Standalone	https://beast.community
Snippy	A pipeline for rapid variant calling and core genome alignment using raw sequencing reads (FASTQ) or genome assemblies (FASTA)	Standalone	https://github.com/tseemann/snippy
Lyve-SET	A high-quality SNP pipeline to create a phylogeny using raw sequencing reads (FASTQ)	Standalone	https://github.com/lskatz/lyve-SET
SNVPhyl	A pipeline for identifying high-quality SNPs and constructing a phylogenetic tree using raw sequencing reads (FASTQ)	Standalone	https://snvphyl.readthedocs.io
CSI Phylogeny	Identifying variant and inferring phylogenies based on the concatenated alignment of the high-quality SNPs using raw sequencing reads (FASTQ) or genome assemblies (FASTA)	Web	https://cge.cbs.dtu.dk/services/CSIPhylogeny
BacWGSTdb	A one-stop platform for bacterial whole-genome sequence typing and source tracking using genome assemblies (FASTA)	Web	http://bacdb.cn/BacWGSTdb

6.参考：

血清型_百度百科

汇总 | 基于全基因组测序数据的细菌分型方法

https://actamicro.ijournals.cn/actamicrocn/article/html/20220316

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Github中文镜像_github镜像知乎

1.介绍