Useful Links and Tools

Under consistent updating …

Bioinformatics Related Journals

• Genome Biology
• Bioinformatics
• Nucleic Acids Research
• Briefings in Bioinformatics
• Genome Research
• Nature Communication
• Nature Biotechnology
• Cell Systems
• Nature Method
• Plos Computational Biology

Tutorials and Lectures materials

• Notes by Ben Langmead lab
  • http://www.langmead-lab.org/teaching-materials/
  • https://github.com/BenLangmead/comp-genomics-class
  • https://github.com/BenLangmead/ads1-notebooks
• Tutorials
  • Computational Genomics
    • https://compgenomr.github.io/book/
  • Genomic data analysis
    • http://genomicsclass.github.io/book/
    • https://liulab-dfci.github.io/bioinfo-combio/
    • https://biocellgen-public.svi.edu.au/mig_2019_scrnaseq-workshop/public/index.html
  • R programming related
    • https://adv-r.hadley.nz/
    • https://bookdown.org/yihui/rmarkdown-cookbook/
    • https://bookdown.org/rdpeng/RProgDA/

Softwares/tools

Useful links

• JHU’s software list https://ccb.jhu.edu/software.shtml

List of tools curated by others

• https://github.com/xhqsm/best-of-bioinformatics
• https://github.com/openbiox/awosome-bioinformatics

Bioconductor workflow packages

• https://www.bioconductor.org/packages/release/BiocViews.html#___Workflow

Review/Benchmark study

• Reads mapping
  • Simulation-based comprehensive benchmarking of RNA-seq aligners https://www.nature.com/articles/nmeth.4106
• Metagenomics classification
  • LEMMI: A continuous benchmarking platform for metagenomics classifiers https://genome.cshlp.org/content/early/2020/07/01/gr.260398.119
• General RNA-seq analysis
  • A survey of best practices for RNA-seq data analysis https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8
• Alternative splicing analysis - Systematic evaluation of differential splicing tools for RNA-seq studies - https://academic.oup.com/bib/article/21/6/2052/5648232
• Chimeric RNA detection
  • 2019-Genome-Biology-Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods
  • https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1842-9
• Structural Variation calling from DNA-seq data
  • 2019-Genome-Biology-Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing
  • https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1720-5
  • 2019-Nature-Communication-Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software
  • https://www.nature.com/articles/s41467-019-11146-4
• Methylation analysis

Data Resources

Reference sequence and annotation

• https://hgdownload.soe.ucsc.edu/downloads.html
• https://uswest.ensembl.org/info/data/ftp/index.html
• https://www.gencodegenes.org/

Datasets

• GEO