gshiba/bio

bio

UMI-tools/umi_tools

• http://genome.cshlp.org/content/early/2017/01/18/gr.209601.116.abstract

genome/pindel

• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781750/

ekg/freebayes

• https://arxiv.org/abs/1207.3907

CAPP-seq / iDES

• https://cappseq.stanford.edu
• sourcecode available but restrictive license

Ensembl

• March 2017 Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation https://academic.oup.com/database/article-lookup/doi/10.1093/database/bax020

Groups

• European Bioinformatics Institute EBI
  • EU > European Moleculary Biology Laboratory EMBL > EBI
• Human Genome Project HGP 1990~
  • Funded by NIH + world
• Ensembl 1999~
  • joint project between European Bioinformatics Institute EBI and Wellcome Trust Sanger Institute
  • response to imminent completion of HGP
• The Cancer Genome Atlas TCGA
  • US Dept of Health and Human Services > National Institutes of Health NIH > National Cancer Institute NCI
• Cancer Genome Project CGP
  • UK > Wellcome Trust Sanger Institute
  • Catalogue of Somatic Mutations in Cancer COSMIC database
    • Curates data from:
      • literature
      • screening projects from CGP
• International Cancer Genome Consortium ICGC 2008~
  • Funded by participating nations; secretariat is the Ontario Institute for Cancer Research OICR
• University of California, Santa Crus UCSC
  • UCSC Genome Browser
    • Originally for distribution of GHP results
  • Other tools: BLAT, liftOver
• National Center for Biotechnology Information NCBI
  • US > NIH > National Library of Medicine NLM> NCBI
  • directed by BLAST author (David Lipman)
  • Databases (all are available through the Entrez search engine):
    • GenBank -- DNA sequences
    • PubMed -- literature
    • dbSNP
• BioMart
  • Community-driven; originated at EBI
• International HapMap Project 2002~
  • world non-/for-profit groups, added ~10 million entries to dbSNP
  • shut down 2016-06-16
• 1000 Genomes Project 1KGP 2008~2015
  • catalogue of variants within and among ethnic groups

Genome browsers

• Ensembl
• NCBI
• UCSC

Databases

• GenBank
  • ...

Tools

SeqMonk

• http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/

Dashboards / Dataviz

Keen IO

• bootstrap dashboard template; plotly; d3js
• https://github.com/keen/dashboards