Genomecomb is a package designed for the analysis of complete genome data. It can be used to compare, annotate and especially filter the results of complete genome sequencing.
In addition to providing installation directives, extensive documentation, we also provide a shortlist of common "protocols" used to analyse whole genome sequencing data. A short list of analyses that can be performed using GenomeComb is given below:
We have used GenomeComb to analyse the whole genome sequences of monozygotic twin genomes, tumor-normal genomes and publicly available HapMap genomes. A publication has about this study appearedin Nature Biotch:
Reumers, J*, De Rijk, P*, Zhao, H, Liekens, A, Smeets, D, Cleary, J, Van Loo, P, Van Den Bossche, M, Catthoor, K, Sabbe, B, Despierre, E, Vergote, I, Hilbush, B, Lambrechts, D and Del-Favero, J
Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing.
Nature biotechnology, 30, 61-88
For the homwes tool available in genomecomb the folowing paper should be referenced
Kancheva,D, Atkinson,D, De Rijk,P, Zimon,M, Chamova,T, Mitev,V, Yaramis,A, Maria Fabrizi,G, Topaloglu,H, Tournev,I, Parma, Y, Battaloglu, E, Estrada-Cuzcano, A, Jordanova, A (2015)
Novel mutations in genes causing hereditary spastic paraplegia and Charcot-Marie-Tooth neuropathy identified by an optimized protocol for homozygosity mapping based on whole-exome sequencing.
Genet. Med., 10.1038
This software is available under the conditions of the GPL