GenomeComb

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Scientific applications

Filter Selection

Supplementary Data Reumers, De Rijk et al

Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

GenomeComb

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Synopsis

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.

Main features

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:

• Import data from the most common sequencing platforms (Complete Genomics, Illumina, SOLiD) and standard variant files (VCF format)
• Compare whole genome sequences, both on the level of variants and sequenced regions in the genome
• Extensive annotation, using publicly available data (e.g. UCSC tracks) or custom annotation tracks
• Powerful queries on variant and genome region data files, optimized for speed and data access, to be able to handle the large data (several gigabytes) generated in whole genome sequencing
• Quantification of the sequenced and filtered regions in a genome
• Set operations on genome regions and variant files: compare, join, subtract
• Automated primer design for Sanger or Sequenom validation directly from the variant files

News

• 2018-03-26 version 0.98.8: some small bugfixes
• 2018-03-07 version 0.98.7 is out: big release (moving towards 1.0)
• 2016-06-22 version 0.90.0 is out: interim release adding structural variant calling for CG data (big changes coming in next version).
• 2015-07-06 version 0.11.0 is out with (a.o.) homwes implementation.
• 2015-04-10 version 0.10.0 is out with many new features.
• 2014-02-19 version 0.9.0 is out with many new features.
• 2012-05-01 version 0.8.5 is out.

Scientific applications

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
pubmed 22178994

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
pubmed 26492578

License

This software is available under the conditions of the GPL