Bioinformatics 101: DNA Sequence Analysis

Genome Visualization Tools:

• UCSC Genome Browser
• popular, free genomic visualization tool for a wide variety of organisms
• also serves as a database for genomic sequences and features
• Integrative Genomics Viewer (IGV)
• very efficient tool for visualizing almost any type of genomic data
• open-source
• Gbrowse - open-source genome browser
• Circos
• circular genome plot
• Especially useful for plotting genomic interaction results
• official code has a step learning curve, but you have a lot of options for precise formatting
• also implemented in Rcircos
• POMO
• creates image similar to circos plot
• I consider the input file much more intuitive than circos configuration files, and plots are created via web interface (instead of local installation)
• can be used to plot data from multiple species
• I would recommend using Firefox; I've had some problems with Chrome and IE

Sequence Alignment:

• BLAST - search for similar DNA sequences in GenBank
• ClustalW - multi-species genome alignment
• TCoffee - multi-species genome alignment
• Mauve - multi-species alignment and visualization tool to detect segments of conserved sequence

General DNA-Seq Tools:

• samtools
• popular, free tool to extract data from .SAM alignment files
• Picard - java-based version of samtools
• see short read aligners necessary for upstream analysis
• Galaxy
• open-source, cloud-based suite of popular sequence analysis tools (including deep sequencing analysis 
• GATK
• toolkit for analysis of next-generation sequencing data
• previously open-source, but now requires a commercial license
• CLC Bio Genomics Workbench
• commercial software covering a wide variety of applications such as sequence alignment, SNP/DIP detection, de novo assembly, etc.
• CLC Bio Genomics Workbench also has the functionality of CLC Bio Main Workbench for standard sequencing analysis (cloning, primer design, etc.)
• both are commercial programs that require a purchased license
• SeqAnswers Software List

Copy Number / Indel Tools:

• CoNIFER
• My favorite tool for making copy number calls in exon capture data
• However, you will want to analyze a pool of samples (say >10) because it is not ideal for analysis of one or two samples. Can also create .bed files to import into DNAcopy.
• PennCNV
• Suite of tools for calling copy number alterations from microarray data
• Includes segmentation algorithm that considers LRR and BAF values
• PennCNV-Affy is particularly useful for processing Affy SNP chip data
• PennCNV2 is designed to handle tumor-normal paired data, but I currently prefer the single-sample analysis from the original PennCNV package
• ASCAT
• Tool for calling somatic copy number alterations from SNP chip data
• estimates tumor purity
• DNAcopy
• Bioconductor package that makes copy number calls (either for single sample or log2ratio for paired samples).
• Works for either microarray or NGS data
• ExomeCopy
• Bioconductor that can make copy number calls directly from .bam files.
• I have found it most useful to produce copy number counts that I can then use for analysis in DNAcopy
• Nexus Copy Number
• commercial software for analysis of copy number alterations
• works for a variety of microarray platforms as well as for deep sequencing analysis
• VarScan
• Can make copy number calls for individual or paired samples (as well as SNP/small indel calls). 
• Individual copy number calls is basically the same as a .pileup file, but somatic calls are relatively useful

Transcription Factor Motif Analysis:

• TRANSFAC
• database of transcription factor motifs
• a subscription is required to access the most recent annotations, but older versions are freely available
• A plug-in is available within CLC Bio (a commercial program for genomics analysis)
• JASPAR
• free database of transcription factor motif sequences
• TFsitescan
• free tool to search for transcription factor motifs
• MEME Suite
• tools for ab initio motif finding
• rVista / VISTA Suite
• tool for searching motifs conserved across closely related organisms
• TESS
  • transcription factor search system
  • unfortunately, this tool now has to be run locally

Mutation Analysis:

• VarScan
• open-source variant calling tool
• see short read aligners necessary for upstream analysis
• usually also requires something like samtools to create input file (.pileup file)
• SeattleSNPs Genome Variation Server
• tool to filter candidate variants (based upon frequency, predicted function, etc.)
• ANNOVAR (pronounced Anno-Var)
• tool to filter candidate variants (based upon frequency, predicted function, etc.)
•  wANNOVAR is the web-based interface
• GWAS Catalog
• NHGRI database of SNP-based phenotypic / disease associations
• Promethease
• open-source tool for personalized genomic analysis
• it is technically free to use, but you can pay $5 to get your report more quickly
• uses annotations from SNPedia
• Interpretome
• Genome interpretation tool similar to Promethease
• In my opinion, nicer interface.  However, it currently only works with raw data from 23andMe and  Lumigenix.
• SNPedia
• crowd sourced annotation of SNP associations
• includes some publicly available genomes
• Geno2MP
• Resource to look up information about rare variants
• DECIPHER
• Resource to look up clinical variant annotation (including copy number alterations)

ChIP-Seq Tools:

• List of tools from the Swiss Institute of Bioinformatics
• MAT peak calling algorithm
• There is an open-source implementation as well as a GUI-based implementation in various programs (like Partek Genomics Suite, a commercial program)

de novo Assembly Algorithms:

• Velvet
• Celera Assembler
• SSAKE
• SOAPdenovo
• FLASh - tool for combining overlapping paired-end reads

Other Tools:

• Primer3 - PCR primer design
• Repeatmasker - identifies repetitive elements within a DNA sequence
• Webcutter - detects restriction enzyme sites in a DNA sequence
• Translate - a tool that allows translation of nucleotide (DNA / RNA) sequence into a protein sequence