Sequence Analysis
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 |