DNA+Sequence+Assembly+Software

DNA Sequence Assembly Contig Assembly

free and open source assembly programs http://sequenceassembly.com/
 * Gap4 / Gap5 || Open source sequence assembler for Sanger sequencing. Part of the Staden package of DNA sequence analysis tools. ||
 * [|Phrap] || The sequence assembly program Phrap was developed to assemble shotgun cosmid and BAC sequencing projects in the Human Genome Project. Phrap pioneered a number of important idea, including the automatic use of entire sequences without trimming and accurate consensus sequences based on sequence qualities and confirmation by other reads.

Free for academic research use. ||
 * Celera Assembler || The program that was used to assemble the first human genome, released as open source in 2004. Assembles Sanger sequencing data and Roche 454 data. ||
 * Arachne || A whole genome assembler for Sanger sequencing reads developed at the Broad Institute. Free for research and educational use. ||
 * ALLPATH || A sequence assembly program for whole genome assemblies from short ("next generation") sequencing reads from MIT's Broad Institute. Free for research and educational use. ||
 * MUMmer || An open source software package for aligning whole genomes. ||
 * AMOS || **A M**odular, **O**pen **S**ource whole genome assembler. A collaboration of four research institutes. ||

The Sanger Institute also has software to download http://www.sanger.ac.uk/resources/software/

see also http://en.wikipedia.org/wiki/Sequence_assembly#Available_assemblers

Here's a paper about sequence assembly Sequence assembly demystified http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg3367.html?WT.mc_id=TWT_NatureRevGenet

see also Online sequence assembly