Bioinformatics Reading Group

Department of Biological Sciences, Clemson University

Thursday, November 1, 2012

Nov. 5, 2012






Topic: Transcriptome assembly

Discussion leader:  Yash

Papers:  Martin and Wang 2011
             Sun et al. 2012

Discussion questions
Labels: Assembly, NGS

No comments:

Post a Comment

Newer Post Older Post Home
Subscribe to: Post Comments (Atom)

Resources

  • Spring 2013 Schedule
  • Fall 2012 Schedule
  • How Illumina works (slide set)
  • RNAseq experimental design
  • Seqanswers forum

Software: Quality checking and filtering

  • ConDeTri
  • FastQC
  • HomerTools
  • NGS QC Toolkit
  • Prinseq
  • Tagcleaner
  • Trimmomatic

Software: Short read assembly

  • Cufflinks
  • Trinity
  • Allpaths-LG
  • IDBA
  • ABySS
  • trans-ABySS
  • SOAPdenovo
  • Velvet

Software: Genotype-by-sequencing

  • Stacks
  • Tassel

Bioinformatics Educational Sites

  • PLoS educational collection
  • Rosalind
  • EMBL tutorials
  • Boston College genomics course

Wells Lab protocols and scripts

  • In silico whole genome digests
  • Using FastQC to assess read quality
  • Merging left- and right-hand fastq reads
  • Sample bash script for Trinity on Palmetto Cluster
  • Preparing Trinity output for Blast2GO annotation
  • Setting up a local blast database of Trinity contigs
  • Tophat/Cufflinks pipeline

Short Courses and Training

  • Cold Spring Harbor Labs
  • Bioinformatics.org online courses
  • University of Manchester
  • UC Davis Short Course
  • UC San Diego online course
Awesome Inc. theme. Powered by Blogger.