DEEP SEQUENCING ANALYSIS SOFTWARE

FastQC Checks quality scores, per base content, over-represented sequences
RNA-SeQC Checks rRNA content, exon/intron/intergenic counts, 5'/3' bias
preseq Estimates and predicts library complexity
CummeRbund R package to visualize Cufflinks data
SeqMonk Java package to visualize mapped reads (interactive scatter/MA plots)
   
DAVID Web based GO analysis with extensive gene ID mapping
blast2go Java program to assign GO terms to novel genes
goseq R package for GO analysis that normalizes for gene length 
   
BEDTools  
HTSeq  
   
SAMtools  
Picard  
BamTools  
FASTX-Toolkit  
SRA Toolkit  
bam2fastq  
   
Galaxy  
GenePattern  
bpipe  
moa  
   

BALTIMORE AREA SEQUENCING

Next Generation Sequencing Center (CRB II 131)
GRCF High Throughput Sequencing Center (Blalock 1005)
JHMI Deep Sequencing & Microarray Core (Broadway 351)
Center for Computational Genomics 
 

USEFUL REFERENCES

SEQanswers (removing duplicates, TopHat MAPQ, cuffmerge vs cuffcompare)
Biostar
Galaxy's mailing list search
Illumina's video of how image data is acquired and initially analyzed
Importance of spike-ins (pmid 23101621)
Synthetic spike-in standards for RNA-seq experiments (pmid 21816910)
Transcription or translation (pmid 21593866)
Transcript quantification models
Rafalab Videos
 

TRAINING AND TUTORIALS

mRNA-Seq using TopHat and Cufflinks (pmid 22383036)
RNA-Seq using raw count based methods like DESeq/edgeR (pmid 23975260)
small RNA sequencing experiments (pmid 21356093)
 
Short Courses and Workshops @JHMI CCG
CGRL @UC Berkeley
Bioinformatics Training Program @UC Davis
Berkeley *Seq
Bioinformatics Organization Educational Services
Australian consortium's NGS workshop notes and Bioinformatics Training Platform
Stephen Turner's list of bioinformatics workshops and resources
 
Unix and Perl Primer for Biologists (by Keith Bradnam and Ian Korf)
Galaxy 101
Python track at Codeacademy
 

OTHER USEFUL SOFTWARE

TextWrangler Free text editor with Perl Compatible Regular Expressions
Cyberduck Free SFTP client
DEVONthink Electronic notebook
Yojimbo Electronic junk drawer
Things Task manager
OmniPlan Project management
Quicksilver Swiss-army knife