8.6. Genomic sequence assembly

Standards and tools for genome sequence assembly and analysis are constantly improving and the best strategy for carrying out a genome project is often through collaboration or through mimicking the protocols and computational strategies used by a recent genome project of similar scope (genome size, budget for sequencing and informatics, etc.). Accordingly, we will not list specific pipelines for these processes, but can direct researchers to sites such as http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational-, http://bioinformatics.igm.jhmi.edu/salzberg/Salzberg/Software.html, and http://soap.genomics.org.cn/soapdenovo.html. Of these options, whole-genome assemblies using the ALLPATHS-LG method (the first link above for the Broad Institute) have been highly successful for both microbes and higher organisms, and this method is arguably the tool of choice currently.