TY - JOUR
T1 - gplas
T2 - a comprehensive tool for plasmid analysis using short-read graphs
AU - Arredondo-Alonso, Sergio
AU - Bootsma, Martin
AU - Hein, Yaïr
AU - Rogers, Malbert R.C.
AU - Corander, Jukka
AU - Willems, Rob J.L.
AU - Schürch, Anita C.
N1 - Publisher Copyright:
© 2020 The Author(s) 2020. Published by Oxford University Press.
PY - 2020/6/15
Y1 - 2020/6/15
N2 - Plasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data are often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and network partitioning based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short-read sequence data.
AB - Plasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data are often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and network partitioning based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short-read sequence data.
UR - http://www.scopus.com/inward/record.url?scp=85087320714&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btaa233
DO - 10.1093/bioinformatics/btaa233
M3 - Article
C2 - 32271863
AN - SCOPUS:85087320714
SN - 1367-4811
VL - 36
SP - 3874
EP - 3876
JO - Bioinformatics (Oxford, England)
JF - Bioinformatics (Oxford, England)
IS - 12
ER -