softwares.md

Bioinformatics - Extra Resources

Software Documentation

• Install CLI tools with BioConda package manager
• Circos
• OpenGene Libraries
• GATK Tools
• ADAM Big-Data Genomics
• FastQC
• samtools 1:BioBits' 2:DaveTang's 3:YanhuiFan's 4:BinaryFlags
• bcftools 1:GATK 2:DaveTang's 3:Paper
• bedtools 1:Quinlan 2:YanhuiFan's
• BWA
• bowtie2
• Tuxedo Suite 1:YanhuiFan's
• bedops
• picard
• jvarkit
• Exomiser disease causing variants
• PopSV structural variants
• Silva silent mutations
• Variant Effect Predictor
• ANNOVAR
• BioGPS
• ABySS
• GEMINI annotation db
• Graphical User Interface (GUI) apps
  • Integrative Genomics Viewer (IGV)
  • NCBI Genome Workbench
  • Savant
  • JBrowse

Other Non-specific Tools

• Atom modern text editor
• Reference Manager
• Git Version Control
  • HowTo Guide
  • Try Online
  • Pro Book
  • Short Videos
  • Start Contributing Guide
• LaTeX
• Overleaf write collaboratively
• Markdown
  • Here
• RegEx Generator
• RegEx 101
• RegEx Debugger
• Plotly
• Small (bioinformatic) Tools Manifesto
• Terminal Multiplexer
• ZSH
• VIM o rather run 'vimtutor' :P
• ShellCheck your scripts
• Writing
  • Correct your Grammar
  • Look-up word by its meaning
  • LanguageTool
  • google translate, obviusly.
• Introduction to HTML