Nescent ngs 2011:Notebook/nescent ngs 2011

Welcome!

• Share notes and comments from the course and beyond!

• Nescent hosted course materials are here
• I found this page very helpful in just getting started
• Helpful notes and tutorials from the MSU course are here
• More from a Broad Institute workshop here
• Some more notes
• Here's a nice overview of a basic alignment and variant calling workflow based on SAMtools and GATK
• A more in-depth variant detection strategy based on GATK
• GAGE

Notes

Please add notes by topic (note that some tools can be used in more than one analysis step):

• Library prep and platform related
• Quality Control and pre-processing
  • HTSeq
  • PRINSEQ
  • FASTX-Toolkit
  • Quake
• Assembly, de novo
  • SOAPdenovo
• Alignment with a reference genome
  • Bowtie2
  • BWA - Burrows-Wheeler Aligner, fast and robust
  • GSNAP
  • SMALT
  • Novoalign - primarily useful for resequencing (i.e. aligning against a very similar reference genome)
  • SOAPaligner/SOAP2
  • Stampy
  • kmer package
  • Mosaik
    • How do you assess/compare the quality of your assembly? Here's one way, from Assemblathon 2010
• Scaffolder
  • Bambus 2
• RAD
  • the wiki
• Gene discovery and annotation
• Variant calling
  • SAMtools
  • Picard
  • bedtools
  • GATK (but also check out their community site)
  • snpEff
  • FreeBayes
  • Syzygy for pooled sequencing
  • PLINK/SEQ
• RNA-seq
• Phylogenomics
• Further analyses
• Visualization
  • IGV
  • Tablet

Useful Links

• BioStar
• Galaxy main
• SEQanswers Wiki

Recent changes