RT Journal Article
SR Electronic
T1 kASA: Taxonomic Analysis of Metagenomic Data on a Notebook
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 713966
DO 10.1101/713966
A1 Silvio Weging
A1 Andreas Gogol-Döring
A1 Ivo Grosse
YR 2020
UL http://biorxiv.org/content/early/2020/05/23/713966.abstract
AB The taxonomic analysis of sequencing data has become important in many areas of life sciences. However, currently available software tools for that purpose either consume large amounts of RAM or yield an insufficient quality of the results.Here we present kASA, a k-mer based software capable of identifying and profiling metagenomic DNA sequences with high computational efficiency and a user-definable memory footprint. We ensure both high sensitivity and precision by using an amino acid-like encoding of k-mers with a dynamic length of multiple k’s. Custom algorithms and data structures optimized for external memory storage enable for the first time a full-scale metagenomic analysis without compromise on a standard notebook.Competing Interest StatementThe authors have declared no competing interest.RAMRandom Access MemoryLCALowest Common AncestorSSDSolid State DriveHDDHard Disk DriveI/OIn- and OutputNGSNext Generation SequencingHPCCHigh Performance Computing Cluster