Genome Assembly Tools

• Newbler, is a software package for de novo DNA sequence assembly
• Celera WGS Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler
• Velvet: Algorithms for de novo short read using de Bruijn graphs
• ALLPATHS: de novo assembly of whole-genome shotgun microreads

• TopHat is a fast splice junction mapper for RNA-Seq reads
• Bowtie is an ultrafast, memory-efficient short read aligner
• SAMtools, SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments
• Avadis NGS is the data mining and visualization platform at the core of all bioinformatics products developed by Strand Scientific Intelligence
• CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of Next Generation Sequencing data
• Cufflinks, assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples

Generic Sequence Assembly and Analysis Tools

• GATK, Broad’s GATK (Genome Analysis Toolkit)
• Galaxy metagenomic pipeline
• SHARCGS, short read assembler based on robust contig extension for genomic sequences
• TGICL, formerly developed at TIGR, now J. Craig Venture Institute
• OASES, developed at EMBL-EBI
• MIRA, developed by Bastien Chevreux
• CAP, developed by Dr. Xiaoqiu Huang at Iowa State University
• SEQCLEAN, now at Harvard University
• TIGR Assembler, now at J. Craig Venture Institute
• RepeatMasker, now at Institute of Systems Biology
• PHRAP, developed by Dr. Phil Green at University of Washington
• fasta, developed by Dr. Bill Pearson at the University of Virginia
• Blat for quick short sequence/genome-to-genome blasting, search, and alignment
• InterProScan for protein signatures in unigenes
• TRF for tandem repeats finder
• More assembly programs to be tested
• Cytoscape for network visulization and display
• Sequence file format for DNA sequence bioinformatics processing
• The sequence manipulation suite