Bioinformatics

Table of Contents

• Bioinformatician
• Bioinformatics
• 生物信息杂谈
• Talks
• Online courses
• Workshop
• Comprehensive packages
• General file formats
• bam/sam/tabix/bgzf
• Fasta/q
• GFF/BED/VCF
• Others formats
• Database API
• data structure
• Models
• Scripts
• Visualization
  • Circos Related
  • Others
• Kmer
• Phylogenetic tree
• Taxonomy
• Assembly
• Alignment
• Multiple Alignment
• Mapping
• Bacterial comparative genomics
• Metagenomics
• 16S
• Classifier | removing human reads
• Virome
• Chip-seq
• Plastform
• PCR
• HPC
• Transcriptome
• Variant Calling

Bioinformatician

• What is a bioinformatician
• Benjamin Franklin Award for Open Access in the Life Sciences
• My Formula as a Bioinformatician
• So you want to be a computational biologist? ☆
• Bioinformatics is not something you are taught, it’s a way of life
• A guide for the lonely bioinformatician
• Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies
• Top N Reasons To Do A Ph.D. or Post-Doc in Bioinformatics/Computational Biology
• 101 Questions: a new series of interviews with notable bioinformaticians
• 生物信息学家级别 Levels of Bioinformatics Research
• It’s time to reboot bioinformatics education
• An Explosion Of Bioinformatics Careers
• Is going back to the wet lab worth it?
• 5 things I wish I knew when I started getting into bioinformatics

Social media

• Staying Current in Bioinformatics & Genomics: 2017 Edition
• Interesting bioinformatics blogs (2017 edition)

Programming skills

• An Introduction to Programming for Bioscientists: A Python-Based Primer
• You can code, too!

Bioinformatics

• The Phylogeny of Everything, the Origin of Eukaryotes, and the Rules of Taxonomy: Death to Archaea, Bacteria, and Eucarya! Long live Archaebacteria, Eubacteria, Eukaryota, and Prokaryota!
• Crossroads (iii) – a New Direction for Bioinformatics with Twelve Fundamental Problems
• Ten Simple Rules for Effective Computational Research（高效计算科学研究的十条简单规则）
• Ten Simple Rules for Reproducible Computational Research
• Ten Simple Rules for the Care and Feeding of Scientific Data
• An Introduction To Applied Bioinformatics
• Freedom in bioinformatics
• 二代测序数据辨（之一）：Clean Data
• 病原微生物高通量测序数据分析笔记
• What to do with lots of (sequencing) data
• The myths of bioinformatics software
• Good Habit for Bioinformatics Analyst or Scientist
• What Are The Most Common Stupid Mistakes In Bioinformatics?
• Myths about Bioinformatics

生物信息杂谈

• 《学生物的，不会编程，也可以报考生物信息学的研究生》by 牛登科。（学生物的，不会编程，也能学生物信息学技术）
• 《高通量测序能替代PCR吗？》 by 韩建
• 《生物信息学数据分析与皇帝的新装》
• 个性化医疗会带来更昂贵的药物？
• 高通量测序公司靠什么赚钱？
• 生物不退学指南：教你如何靠生物养家糊口 （想进入生物学领域的请看）

Talks

• How NGS is transforming medicine

Online courses

• Rosalind (Rosalind is a platform for learning bioinformatics through problem solving)
• Teaching Materials of Langmead-lab

Workshop

• Next-Gen Sequence Analysis Workshop

Book

• A Primer for Computational Biology

Comprehensive packages

• [python] Biopython
• [golang] Biogo
• [golang] bio - A simple but high-performance bioinformatics package in Go

General file formats

• zindex - Create an index on a compressed text file
• tabix  - table file index
• wormtable - Write-once-read-many table for large datasets.

bam/sam/tabix/bgzf

• [python] hts-python - pythonic wrapper for libhts
• [python] htseq - HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. http://www-huber.embl.de/users/anders/HTSeq/
• [golang] biogo/hts
• bamtools - C++ API & command-line toolkit for working with BAM data
• samblaster -  a tool to mark duplicates and extract discordant and split reads from sam files.
• [python] pysamstats - A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
• [python] pysam - a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. Another sam parser: simplesam
• grabix - a wee tool for random access into BGZF files
• [golang]  bix - tabix file access with golang using biogo machinery
• mergesam - Automate common sam & bam conversions
• SAMstat - Displaying sequence statistics for next generation sequencing

Fasta/q

• seqtk - Toolkit for processing sequences in FASTA/Q formats
• seqkit - A cross-platform and efficient toolkit for FASTA/Q file manipulation http://bioinf.shenwei.me/seqkit
• [python] pyfaidx - pyfaidx: efficient pythonic random access to fasta subsequences
• [golang] bio - A lightweight and high-performance bioinformatics package in Go

FASTA index

• [golang] faidx
• [golang] bio/seqio/fai

GFF/BED/VCF

• bedtools2 - A powerful toolset for genome arithmetic.
• BEDOPS - the fast, highly scalable and easily-parallelizable genome analysis toolkit
• [python] gffutils - GFF and GTF file manipulation and interconversion
• [python] pybedtools - Python wrapper for Aaron Quinlan's BEDTools
• [golang] irelate - Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang
• [golang] vcfgo - a golang library to read, write and manipulate files in the variant call format.
• vcflib - a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

Others formats

• blast_table2xml - Convert blast m6 format to xml for blast2go
• seqmagick - file format conversion in Biopython in a convenient way

Database API

• pyensembl - Python interface to ensembl reference genome metadata (exons, transcripts, etc...)

data structure

• kvector - kvector is a small utility for converting motifs to kmer vectors to compare motifs of different lengths

Models

• pomegranate - Graphical models for Python, implemented in Cython for speed.

Scripts

• oneliners - Useful bash one-liners for bioinformatics.
• cgat - CGAT - Computational Genomics Analysis Tools
• bcbb - Incubator for useful bioinformatics code, primarily in Python and R http://bcbio.wordpress.com
• jcvi - Python utility libraries on genome assembly, annotation and comparative genomics
• picobio - Miscellaneous Bioinformatics scripts etc mostly in Python
• pydna - Classes and code for representing double stranded DNA and functions for simulating homologous recombination and Gibson assembly.
• BioUtils - Python scripts for miscellaneous bioinformatics stuff.
• sesbio - Bioinformatics scripts for genome analysis
• ngsutils - Tools for next-generation sequencing analysis http://ngsutils.org
• ngsTools - Programs to analyse NGS data for population genetics purposes

Visualization

• Circleator - Flexible circular visualization of genome-associated data with BioPerl and SVG.
• ComplexHeatmap - make complex heatmaps as well as self define annotation graphics
• dalliance - Interactive web-based genome browser. http://www.biodalliance.org/
• Question: Which program, tool, or strategy do you use to visualize genomic rearrangements? 
• DNAplotlib - DNA plotting library for Python

Circos Related

• Circos: Perl package for circular plots, which are well suited for genomic rearrangements.
• J-Circos is a java application for doing interactive work with circos plots.
• ClicO FS: an interactive web-based service of Circos.
• rCircos: R package for circular plots. [last update: 2013]
• OmicCircos: R package for circular plots for omics data.[last update: 2015-04]

Gene Annotation

• Gviz - Plotting data and annotation information along genomic coordinates
• pyGenomeTracks - python module to plot beautiful and highly customizable genome browser tracks
• karyoploteR - karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
• gggenes - Draw gene arrow maps in ggplot2

Others

• ggbio: R package for visualizing biological data. Has a circular view similar to the previous packages.
• D3 chord diagrams (javascript) can be used to visualize genomic rearrangements. See this plot of migration flows as a similar example.
• Genomatix Transcriptome Viewer: Gene Fusion analyses
• iFUSE: integrated fusion gene explorer
• FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery
• SOAPFuse includes the option to generate figures
• Gremlin
• Seqeyes: A flash tool for visualizing structural variations.
• SVVIZ - A READ VISUALIZER TO VALIDATE STRUCTURAL VARIANTS
• samplot - Plot structural variant signals from many BAMs and CRAMs

Kmer

• khmer - In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more http://khmer.readthedocs.org/
• Jellyfish

Phylogenetic tree

• [R] ggtree - a phylogenetic tree viewer for different types of tree annotations
• [python] ETE tools
• evolview

Taxonomy

• NCBI_taxonomy_tree - NCBI taxonomy tree in-memory mapping
• taxiphy - Common repository for scripts to generate trees from taxonomies. Currently includes ITIS, NCBI, and GBIF.
• gtaxon - A fast cross-platform NCBI taxonomy data querying (gi2taxid, taxid2taxon, name2taxid, LCA) tool, with cmd client and REST API server for both local and remote server.
• [R] taxize - A taxonomic toolbelt for R http://ropensci.org/tutorials/taxize.html
• TaxonKit - Cross-platform and Efficient NCBI Taxonomy Toolkit http://bioinf.shenwei.me/taxonkit/

Assembly

• Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
• nucleotid.es - an assembler catalogue

Alignment

• hpg-aligner - HPG Aligner is an ultrafast and highly sensitive Next-Generation Sequencing (NGS) mapper which supoprts both DNA and RNA alignment
• AliView - Software for aligning viewing and editing dna/aminoacid sequences, intuitive, fast and lightweight. Download and website: http://www.ormbunkar.se/aliview

Multiple Alignment

• msa: An R Package for Multiple Sequence Alignment

Mapping

Bacterial comparative genomics

• TOOLS FOR BACTERIAL COMPARATIVE GENOMICS

Metagenomics

• shotmap - A Shotgun Metagenome Annotation Pipeline

• metagenomeSeq - Statistical analysis for sparse high-throughput sequencing

• mmgenome - Tools for extracting individual genomes from metagneomes

• harvest - suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes.

• PhyloSift - Phylogenetic and taxonomic analysis for genomes and metagenomes

• MetaQuery: Annotation and quantitative analysis of genes in the human gut microbiome

• Microbial Ecology - a discussion and overview of amplicon sequencing and metagenomics

• Quick Insights from Sequencing Data with sourmash

• Recovering “genomes” from metagenomes

16S

• 高通量数据处理的一些经验和建议
• How to choose ordination method, such as PCA, CA, PCoA, and NMDS?

Classifier | removing human reads

• taxonomer.iobio - Taxonomer is a kmer-based ultrafast metagenomics tool for assigning taxonomy to sequencing reads from both clinical and environmental samples.
• BMTagger - Best Match Tagger for removing human reads from metagenomics datasets paper,sop
• Centrifuge - Classifier for metagenomic sequences

Virome

• viral-ngs - Viral genomics analysis pipelines

Chip-seq

• ChIP-seq-analysis

Plastform

• Rabix - Portable Bioinformatics Pipelines
• bioboxes - Standards for Interchangeable Bioinformatics Containers
• Anvi’o is an analysis and visualization platform for ‘omics data. introduction

PCR

• find_differential_primers - Scripts to aid the design of differential primers for diagnostic PCR.
• Primer3-py - Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.

HPC

• hpcgo - Helping submit jobs to HPC cluster.
• easy_qsub  - Easily submitting PBS jobs with script template. Multiple input files supported.

Transcriptome

• De novo transcriptome assembly

• Annotating and evaluating a de novo transcriptome assembly

• Evaluating your transcriptome assembly

• Differential Expression and Visualization in R

• RNA-seq Analysis

variant calling

one-liner

ensemble id -> symbol -> biotype

zcat Homo_sapiens.GRCh38.84.gtf.gz \
    | awk '$3=="gene"' \
    | perl -ne 'next unless /gene_id "(.+?)".+gene_name "(.+?)".+gene_biotype "(.+?)"/; print "$1\t$2\t$3\n";' \
    > Homo_sapiens.GRCh38.84.gtf.gz.ensemble2symol-biotype.tsv