title: iDoComp: a compression scheme for assembled genomes.
abstract: BACKGROUND
  With the release of the latest next-generation sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing a Human has dropped to a mere $4000. Thus we are approaching a milestone in the sequencing history, known as the $1000 genome era, where the sequencing of individuals is affordable, opening the doors to effective personalized medicine. Massive generation of genomic data, including assembled genomes, is expected in the following years. There is crucial need for compression of genomes guaranteed of performing well simultaneously on different species, from simple bacteria to humans, which will ease their transmission, dissemination and analysis. Further, most of the new genomes to be compressed will correspond to individuals of a species from which a reference already exists on the database. Thus, it is natural to propose compression schemes that assume and exploit the availability of such references.
  
  
  RESULTS
  We propose iDoComp, a compressor of assembled genomes presented in FASTA format that compresses an individual genome using a reference genome for both the compression and the decompression. In terms of compression efficiency, iDoComp outperforms previously proposed algorithms in most of the studied cases, with comparable or better running time. For example, we observe compression gains of up to 60% in several cases, including H.sapiens data, when comparing with the best compression performance among the previously proposed algorithms.
  
  
  BACKGROUND
  iDoComp is written in C and can be downloaded from: http://www.stanford.edu/~iochoa/iDoComp.html (We also provide a full explanation on how to run the program and an example with all the necessary files to run it.).
authors.affiliation: Department of Electrical Engineering, Stanford University, 350 Serra Mall, Stanford, CA.
authors.forename: Idoia
authors.initials: I
authors.lastname: Ochoa
authors.affiliation: Department of Electrical Engineering, Stanford University, 350 Serra Mall, Stanford, CA.
authors.forename: Mikel
authors.initials: M
authors.lastname: Hernaez
authors.affiliation: Department of Electrical Engineering, Stanford University, 350 Serra Mall, Stanford, CA.
authors.forename: Tsachy
authors.initials: T
authors.lastname: Weissman
mesh_terms: D000465:Algorithms; D044962:Data Compression / Q000379:methods*; D016208:Databases, Factual; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D057285:Precision Medicine; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software