电子书

https://cbirt.net/bioinformatics-books/

anneng — Wed, 03 Aug 2022 07:56:34 GMT

生信电子书清单
生信电子书清单

A primer on microbial bioinformatics for nonbioinformaticians

anneng — Mon, 13 Jun 2022 06:27:09 GMT

https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(17)30709-7/fulltext
Table 1List of bioinformatics software used for microbial bioinformatics data analysis
Usage Software name Description URL
Quality measures and read preprocessing FASTQC Toolbox for displaying sequence statistics for next-generation sequencing reads http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
TRIMMOMATIC Command-line based tool for trimming of short-read paired-end and single-ended data http://www.usadellab.org/cms/?page=trimmomatic
FASTX-Toolkit A collection of command line tools for preprocessing of short-read FASTA/FASTQ files http://hannonlab.cshl.edu/fastx_toolkit/
PRINSEQ Command-line and web-based tool for filtering, reformatting, or trimming genomic and metagenomic sequence data, generates summary statistics in graphical and tabular format http://prinseq.sourceforge.net/, http://edwards.sdsu.edu/cgibin/prinseq/prinseq.cgi
Contamination detection Kraken Taxonomic assignment of reads, useful for metagenomics analysis or detection of contamination in pure culture samples https://ccb.jhu.edu/software/kraken/
MIDAS Taxonomic assignment of reads, useful for metagenomics analysis or detection of contamination in pure culture samples https://github.com/snayfach/MIDAS
Assembly software and pipelines Velvet De novo genomic assembler specially designed for short reads http://github.com/dzerbino/velvet/tree/master
SPAdes De novo genomic assembler for short reads; it can also provide hybrid assemblies using long-read data together with short-read data http://cab.spbu.ru/software/spades/
Canu De novo genomic assembler designed for high-noise single-molecule sequencing such as long reads http://github.com/marbl/canu
INNUca A standardized, fully automated, flexible, portable and pathogen-independent pipeline for bacterial genome assembly and quality control starting from short reads http://github.com/INNUENDOCON/INNUca
shovill A pipeline for bacterial genome assembly which improves SPAdes speed and accuracy https://github.com/tseemann/shovill
In silico typing ReMatCh Software for variant calling based on a read-mapping strategy to selected target sequences; also interacts with European Nucleotide Archive (ENA) repository, easily mining publicly available data http://github.com/B-UMMI/ReMatCh
Short Read Sequence Typing for Bacterial Pathogens (SRST2) It uses short-read data, MLST database and/or database of gene sequences (e.g. resistance genes, virulence genes) and reports the presence of STs and/or reference genes http://github.com/katholt/srst2
Microbial InSilico Typer (MIST) Rapid generation of in silico typing data (e.g. MLST, MLVA) from draft bacterial genome assemblies http://bitbucket.org/peterk87/microbialinsilicotyper
SISTR A web- and command line–accessible tool for Salmonella typing using draft genome assemblies http://lfz.corefacility.ca/sistr-app/
SeqSero A web-accessible tool for Salmonella typing using raw reads or draft genome assemblies http://www.denglab.info/SeqSero
RGI-CARD Curated collection of antimicrobial resistance gene and mutation sequences, bioinformatics models and tools for their detection in bacterial genomes http://www.card.mcmaster.ca/analyze/rgi
ResFinder A web-accessible tool for the detection of acquired antimicrobial resistance genes in bacterial genomes using raw reads or draft genome assemblies https://cge.cbs.dtu.dk/services/ResFinder/
VirulenceFinder A web-accessible tool for the detection of virulence associated genes in Escherichia coli, Listeria spp., Staphylococcus aureus, Enterococcus spp. using raw reads or draft genome assemblies https://cge.cbs.dtu.dk/services/VirulenceFinder/
MLST1.8 A web-accessible tool for the determination of MLST types from bacterial genomes using publicly available MLST schemas https://cge.cbs.dtu.dk/services/MLST
Mlst2.9 Command line–based software which can extract MLST from bacterial genomes using publicly available MLST schemas https://github.com/tseemann/mlstCFSANSNP
CFSAN SNP Pipeline Pipeline for extracting high quality SNV matrices for sequences from closely related pathogens http://snppipeline.readthedocs.io/en/latest/
Snippy A pipeline for rapid identification of haploid variants and construction of phylogeny using core genome SNPs http://github.com/tseemann/snippy
SNVPhyl (Single Nucleotide Variant PHYLogenomics) Pipeline for identifying SNV within a collection of microbial genomes and constructing a phylogenetic tree http://snvphyl.readthedocs.io/en/latest/
Lyve-SET A pipeline for using high-quality SNPs to create a phylogeny, especially for outbreak investigations https://github.com/lskatz/lyve-SET
Gene-by-gene approaches BIGSdb Web-accessible database system designed to store and analyse linked phenotypic and genotypic information, including allele calling engine for gene-by-gene approach; it is the database system for both PubMLST and PasteurMLST https://github.com/kjolley/BIGSdb, http://pubmlst.org
http://bigsdb.pasteur.fr/index.html
Enterobase Curated database and online resource for molecular typing of Salmonella, Escherichia coli, Yersinia spp. and Moraxella spp. using gene-by-gene approach http://enterobase.warwick.ac.uk/
Genome Profiler Stand-alone gene-by-gene allele calling algorithm which uses conserved gene neighbourhoods to resolve gene paralogy http://sourceforge.net/projects/genomeprofiler/
chewBBACA A comprehensive and highly efficient stand-alone gene-by-gene allele calling algorithm based on coding DNA sequences, including suite of tools for providing overview of schema performance https://github.com/B-UMMI/chewBBACA
Gene annotation Prodigal Protein-coding gene prediction software tool for bacterial and archaeal genomes http://github.com/hyattpd/prodigal/wiki
Prokka Quick functional annotation of bacterial genomes producing standards-compliant output file http://github.com/tseemann/prokka
RAST Fully automated service for annotating bacterial and archaeal genomes http://rast.nmpdr.org/
MicroScope Comprehensive analytical platform for genome annotation and analysis of bacterial genomes http://www.genoscope.cns.fr/agc/microscope/home/index.php
NCBI prokaryotic genome annotation pipeline (PGAP) Automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology-based methods https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
NCBI Pathogen Detection An online platform for sharing and comparing data on outbreak strains; currently contains databases for 20 bacterial species, focusing on food-borne pathogens and healthcare-associated infections https://www.ncbi.nlm.nih.gov/pathogens/
Genome alignments Harvest A suite of core genome alignment and visualization tools for quick and high-throughput analysis of intraspecific bacterial genomes http://harvest.readthedocs.io/en/latest/
Mauve Aligner for comparative analysis of full bacterial genomes http://darlinglab.org/mauve/mauve.html
Homology clustering and Association studies Roary High speed stand-alone pan-genome pipeline for bacterial genomes http://sanger-pathogens.github.io/Roary/
Scoary Pan-genome–wide association studies using Roary output https://github.com/AdmiralenOla/Scoary
Neptune Software designed for detecting genomic signatures within bacterial populations https://github.com/phac-nml/neptune
Phylogenetic inference RAxML Sequential and parallel maximum-likelihood phylogeny estimation that operates on nucleotide and protein sequence alignments https://sco.h-its.org/exelixis/software.html
FastTree Compute approximately maximum likelihood phylogenetic trees from large nucleotide or protein multiple sequence alignments http://www.microbesonline.org/fasttree/
Gubbins Compute maximum likelihood from alignment after removing regions containing elevated densities of base substitutions https://github.com/sangerpathogens/gubbins
ClonalFrameML A maximum likelihood implementation of ClonalFrame designed for genomes sequences https://github.com/xavierdidelot/ClonalFrameML
PHYLOViZ Online Web-based tool for phylogenetic inference, visualization, analysis and sharing of sequence-based typing methods that generate allelic profiles and associated epidemiologic data http://online.phyloviz.net
PHYLOViZ 2.0 Stand-alone Java software for phylogenetic inference, visualization and analysis of sequence-based typing methods that generate allelic profiles and their associated epidemiologic data http://www.phyloviz.net/
Visualization tools Microreact A web-based tool for genomic epidemiology data visualization and sharing http://microreact.org
Phandango Interactive web-based tool for fast exploration of large-scale population genomics data sets combining output from multiple genomic analysis methods https://github.com/jameshadfield/phandango
iTOL Web-based tool for display, annotation and management of phylogenetic trees http://itol.embl.de/
GenGIS 2 Application including 3-D graphical and Python interfaces allowing users to combine digital map data and sequences http://kiwi.cs.dal.ca/GenGIS/Main_Page
Multipurpose analytical platforms and pipelines Centre for Genomic Epidemiology Toolbox A suite of web-based tools and service for pathogen molecular typing, genome assembly, phenotypic prediction (e.g. resistance prediction) and phylogeny construction http://cge.cbs.dtu.dk/services/
Integrated Rapid Infectious Disease Analysis (IRIDA) Platform A Galaxy-based platform for real-time infectious disease outbreak investigation using genomic data including a sequence data management module and workflows, ontology framework (GenEpiO) and data visualization tools https://irida.corefacility.ca/documentation/downloads/index.html, http://irida.ca/
Integration genomics in surveillance of food-borne pathogens (INNUENDO) platform A platform for real-time disease outbreak investigation and surveillance of food-borne pathogens using genomic data including sequence-data management module, assembly modules with QA/QC measures, gene-by-gene analytical pipeline, ontology framework (GenEpiO) and visualization tools https://github.com/INNUENDOCON/INNUENDO_platform
Nullarbor A pipeline for generating public health microbiology reports from sequenced isolates including sequencing specifics, species ID, subtypes and core SNP http://github.com/tseemann/nullarbor

Medical Microbiology, 4th edition

anneng — Mon, 13 Jun 2022 05:52:12 GMT

https://www.ncbi.nlm.nih.gov/books/NBK7627/

applied bioinformatics 应用生物信息学

anneng — Fri, 10 Jun 2022 06:23:41 GMT

AB.pdf applied bioinformatics 应用生物信息学

Perl

anneng — Mon, 23 May 2022 10:15:32 GMT

https://perlmaven.com/

Modern Statistics for Modern Biology

anneng — Thu, 12 May 2022 02:17:20 GMT

http://web.stanford.edu/class/bios221/book/

All things considered for Bioinformatics

anneng — Wed, 11 May 2022 07:55:43 GMT

https://xie186.github.io/Novice2Expert4Bioinformatics/

Introduction to Modern Statistics

anneng — Mon, 11 Apr 2022 06:06:48 GMT

https://github.com/OpenIntroStat/ims

Melbourne Bioinformatics

anneng — Sat, 26 Mar 2022 06:21:07 GMT

https://www.melbournebioinformatics.org.au/tutorials/

Biomedical Knowledge Mining using GOSemSim and clusterProfiler

anneng — Wed, 23 Mar 2022 10:36:00 GMT

Biomedical Knowledge Mining using GOSemSim and clusterProfiler
http://yulab-smu.top/biomedical-knowledge-mining-book/index.html

进化树

anneng — Thu, 17 Mar 2022 10:16:28 GMT

https://yulab-smu.top/treedata-book/index.html
Data Integration, Manipulation and Visualization of Phylogenetic Trees

RNA 分析

anneng — Thu, 17 Mar 2022 09:22:39 GMT

(Innovations in Big Data and Machine Learning) Dolly Sharma, Shailendra Singh, Mamta Mittal - Bioinformatics and RNA_ A Practice-Based Approach-CRC Press (2021).pdf

Ernesto Picardi - RNA Bioinformatics-Humana (2021).pdf

Basic applied bioinformatics 基础应用生物信息学

anneng — Fri, 11 Mar 2022 03:08:49 GMT

Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal - Basic applied bioinformatics-John Wiley & Sons (2017).pdf
对数据库和blast工具做了比较详细的介绍
""Title Page""
""Table of Contents""
""Preface""
""Acknowledgments""
""List of Abbreviations""
""SECTION I: Molecular Sequences and Structures""
""CHAPTER 1: Retrieval of Sequence(s) from the NCBI Nucleotide Database""
""1.1 INTRODUCTION""
""1.2 COMPONENTS OF THE NCBI NUCLEOTIDE DATABASE""
""1.3 OBJECTIVES""
""1.4 PROCEDURE""
""1.5 SOME USEFUL NUCLEOTIDE SEQUENCE DATABASES OF NCBI""
""1.6 QUESTIONS""
""CHAPTER 2: Retrieval of Protein Sequence from UniProtKB""
""2.1 INTRODUCTION""
""2.2 OBJECTIVE""
""2.3 PROCEDURE""
""2.4 QUESTIONS"" "
"CHAPTER 3: Downloading Protein Structure""""3.1 INTRODUCTION""
""3.2 OBJECTIVE""
""3.3 PROCEDURE""
""3.4 QUESTIONS""
""CHAPTER 4: Visualizing Protein Structure""
""4.1 INTRODUCTION""
""4.2 OBJECTIVE""
""4.3 PROCEDURE""
""4.4 QUESTIONS""
""CHAPTER 5: Sequence Format Conversion""
""5.1 INTRODUCTION""
""5.2 OBJECTIVE""
""5.3 PROCEDURE""
""5.4 QUESTIONS""
""5.5 BRIEF DESCRIPTION OF SOME OF THE IMPORTANT MOLECULAR SEQUENCE FORMATS""
""CHAPTER 6: Nucleotide Sequence Analysis Using Sequence Manipulation Suite (SMS)""
""6.1 INTRODUCTION""
""6.2 OBJECTIVE""
""6.3 PROCEDURE"" ""6.4 FORMAT CONVERSION""""6.5 SEQUENCE ANALYSIS""
""6.6 SEQUENCE FIGURES""
""6.7 RANDOM SEQUENCES""
""6.8 MISCELLANEOUS""
""6.9 QUESTIONS""
""CHAPTER 7: Detection of Restriction Enzyme Sites""
""7.1 INTRODUCTION""
""7.2 OBJECTIVE""
""7.3 PROCEDURE (USING NEBCUTTER)""
""7.4 QUESTIONS""
""SECTION II: Sequence Alignment""
""CHAPTER 8: Dot Plot Analysis""
""8.1 INTRODUCTION""
""8.2 OBJECTIVE""
""8.3 PROCEDURE""
""8.4 PARAMETERS OF DOT PLOT ANALYSIS""
""8.5 INTERPRETATION""
""8.6 QUESTIONS""
""CHAPTER 9: Needlemanâ#x80
#x93
Wunsch Algorithm (Global Alignment)""
""9.1 INTRODUCTION"" ""9.2 OBJECTIVE""""9.3 PROCEDURE""
""9.4 QUESTIONS""
""CHAPTER 10: Smithâ#x80
#x93
Waterman Algorithm (Local Alignment)""
""10.1 INTRODUCTION""
""10.2 OBJECTIVE""
""10.3 PROCEDURE""
""10.4 QUESTIONS""
""CHAPTER 11: Sequence Alignment Using Online Tools""
""11.1 INTRODUCTION""
""11.2 OBJECTIVE""
""11.3 PROCEDURE""
""11.4 INTERPRETATION OF RESULTS""
""11.5 COLOR SCHEME FOR AMINO ACID RESIDUES""
""11.6 QUESTIONS""
""SECTION III: Basic Local Alignment Search Tools""
""CHAPTER 12: Basic Local Alignment Search Tool for Nucleotide (BLASTn)""
""12.1 INTRODUCTION""
""12.2 OBJECTIVE"" ""12.3 PROCEDURE""""12.4 QUESTIONS""
""CHAPTER 13: Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp)""
""13.1 INTRODUCTION""
""13.2 OBJECTIVE""
""13.3 PROCEDURE""
""13.4 QUESTIONS""
""CHAPTER 14: BLASTx""
""14.1 INTRODUCTION""
""14.2 OBJECTIVE""
""14.3 PROCEDURE""
""14.4 INTERPRETATION OF BLASTx RESULTS""
""14.5 QUESTIONS""
""CHAPTER 15: tBLASTn""
""15.1 INTRODUCTION""
""15.2 OBJECTIVE""
""15.3 PROCEDURE""
""15.4 ALGORITHM PARAMETERS""
""15.5 INTERPRETATION OF tBLASTn RESULTS""
""15.6 QUESTIONS""
""CHAPTER 16: tBLASTx""
""16.1 INTRODUCTION""

病毒数据分析相关文献

anneng — Thu, 10 Mar 2022 08:03:16 GMT

VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs
zheng2017 VirusDetect An automated pipeline for efficient virus discovery using deep sequencing of small RNAs.pdf

这个流程包括有参组装、de novo组装、去宿主，使用的是blastn 来扫描一个病毒数据库可以用来进行新病毒的发现或者分析病毒的进化

官网： http://bioinfo.bti.cornell.edu/tool/VirusDetect/
https://github.com/kentnf/VirusDetect
考虑到这个软件是perl开发的我们最好不用直接用里面的软件自己封装成cwl

传统的方法无法识别新病毒或病毒变异
enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), nucleic acid hybridization or microarray are useful but they require prior knowledge or sequence information of the potential pathogens, thus they are not highly efficient in detecting novel viruses or virus variants

整体流程图如下：

1.使用bwa和病毒参考数据库进行比对比对上的序列和参考序列进行有参组装得到病毒的一致性序列这个分支主要用于发现已知病毒
2.使用bwa和宿主进行比对去宿主 (可选步骤) 使用没有map上的序列进行de novo 组装（Velvet ） ‘hash_length’ (the length of k-mer) ‘cov_cutoff’ (the coverage cutoff) 参数会严重影响组装质量因此这个地方尝试了多次最终选择了contig比较长的参数组合这些contig又和宿主进行了比对抛弃比对上的contig （有个宿主基因组会整合病毒序列这种序列活性不高可以删除）
3.整合有参和无参得到的contig 删除重复的contig
4.使用blastn、blastx注释病毒contig 生成sam文件

https://openstax.org/

anneng — Fri, 03 Dec 2021 11:20:52 GMT

https://openstax.org/ 免费的教科书

Data Mining for Bioinformatics

anneng — Wed, 11 Aug 2021 12:39:44 GMT

Data Mining for bioinformatics.pdf
对聚类分类特征提取做了详细介绍

Cloud Data Management

anneng — Mon, 09 Aug 2021 02:59:51 GMT

https://dataschool.com/data-governance/?__hstc=158613477.3a53ee0e16c6e7c0b267c9e09a7ccccf.1628477549021.1628477549021.1628477549021.1&__hssc=158613477.4.1628477549021&__hsfp=3676039252

交互式应用

ice-melt — Fri, 06 Aug 2021 07:02:35 GMT

Plotly_and_Dash.pdf

Mastering_Shiny.pdf

群体遗传学书籍 population genetics

anneng — Tue, 06 Jul 2021 02:56:37 GMT

https://biology.stackexchange.com/questions/16470/books-on-population-or-evolutionary-genetics

Streamlining data-intensive biology with workflow systems

anneng — Mon, 24 May 2021 07:26:36 GMT

giaa140 Streamlining data-intensive biology with workflow systems.pdf

Computational Genomics with R

anneng — Mon, 01 Feb 2021 10:45:59 GMT

https://compgenomr.github.io/book/

数据可视化实战.pdf

anthonyd — Fri, 29 Jan 2021 07:14:15 GMT

数据可视化实战.pdf

https://libretexts.org/

anneng — Mon, 30 Nov 2020 08:39:11 GMT

https://libretexts.org/
各个学科的免费教材

Human Molecular Genetics

anneng — Fri, 20 Nov 2020 02:17:39 GMT

http://libgen.rs/book/index.php?md5=877A856C05EC560967256A9D486078F8
Human Molecular Genetics has been carefully crafted over successive editions to provide an authoritative introduction to the molecular aspects of human genetics, genomics and cell biology.
Maintaining the features that have made previous editions so popular, this fifth edition has been completely updated in line with the latest developments in the field. Older technologies such as cloning and hybridization have been merged and summarized, coverage of newer DNA sequencing technologies has been expanded, and powerful new gene editing and single-cell genomics technologies have been added. The coverage of GWAS, functional genomics, stem cells, and disease modeling has been expanded. Greater focus is given to inheritance and variation in the context of populations and on the role of epigenetics in gene regulation.

Biopython Tutorial and Cookbook

anneng — Wed, 18 Nov 2020 07:58:32 GMT

http://biopython.org/DIST/docs/tutorial/Tutorial.html

生物信息学电子书

anneng — Wed, 05 Aug 2020 03:14:49 GMT

https://bookdown.org/hbsabafaculty/ids_book/