Reference-independent comparative metagenomics using cross-assembly: crAss.
BACKGROUND
Metagenomes are often characterized by high levels of unknown sequences. Reads derived from known microorganisms can easily be identified and analyzed using fast homology search algorithms and a suitable reference database, but the unknown sequences are often ignored in further analyses, biasing conclusions. Nevertheless, it is possible to use more data in a comparative metagenomic analysis by creating a cross-assembly of all reads, i.e. a single assembly of reads from different samples. Comparative metagenomics studies the interrelationships between metagenomes from different samples. Using an assembly algorithm is a fast and intuitive way to link (partially) homologous reads without requiring a database of reference sequences.


RESULTS
Here, we introduce crAss, a novel bioinformatic tool that enables fast simple analysis of cross-assembly files, yielding distances between all metagenomic sample pairs and an insightful image displaying the similarities.
Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands. dutilh@cmbi.ru.nl
Bas E
BE
Dutilh
Robert
R
Schmieder
Jim
J
Nulton
Ben
B
Felts
Peter
P
Salamon
Robert A
RA
Edwards
John L
JL
Mokili
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D016679:Genome, Viral; D006801:Humans; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D012984:Software