FN Archimer Export Format
PT J
TI A comparison of Oxford nanopore library strategies for bacterial genomics
BT 
AF Sauvage, Thomas
   Cormier, Alexandre
   PASSERINI, Delphine
AS 1:1;2:2;3:1;
FF 1:PDG-RBE-MASAE-LEMMMB;2:PDG-IRSI-SEBIMER;3:PDG-RBE-MASAE-LEMMMB;
C1 Ifremer, MASAE Microbiologie Aliment Santé Environnement, F-44000, Nantes, France
   Ifremer, IRSI-SeBiMER, F-29280, Plouzané, France
C2 IFREMER, FRANCE
   IFREMER, FRANCE
SI NANTES
   BREST
SE PDG-RBE-MASAE-LEMMMB
   PDG-IRSI-SEBIMER
IN WOS Ifremer UPR
   DOAJ
IF 4.4
TC 1
UR https://archimer.ifremer.fr/doc/00857/96917/105566.pdf
   https://archimer.ifremer.fr/doc/00857/96917/105567.pdf
   https://archimer.ifremer.fr/doc/00857/96917/105568.pdf
   https://archimer.ifremer.fr/doc/00857/96917/105569.pdf
   https://archimer.ifremer.fr/doc/00857/96917/105570.pdf
   https://archimer.ifremer.fr/doc/00857/96917/105571.pdf
LA English
DT Article
DE ;Hybrid;Native;Leakage;Ligation;Mapping;minION;Tagmentation;Tandem;Transposase;Replicons
AB Background Oxford nanopore Technologies (ONT) provides three main library preparation strategies to sequence bacterial genomes. These include tagmentation (TAG), ligation (LIG) and amplification (PCR). Despite ONT’s recommendations, making an informed decision for preparation choice remains difficult without a side-by-side comparison. Here, we sequenced 12 bacterial strains to examine the overall output of these strategies, including sequencing noise, barcoding efficiency and assembly quality based on mapping to curated genomes established herein. Results Average read length ranged closely for TAG and LIG (> 5,000 bp), while being drastically smaller for PCR (< 1,100 bp). LIG produced the largest output with 33.62 Gbp vs. 11.72 Gbp for TAG and 4.79 Gbp for PCR. PCR produced the most sequencing noise with only 22.7% of reads mappable to the curated genomes, vs. 92.9% for LIG and 87.3% for TAG. Output per channel was most homogenous in LIG and most variable in PCR, while intermediate in TAG. Artifactual tandem content was most abundant in PCR (22.5%) and least in LIG and TAG (0.9% and 2.2%). Basecalling and demultiplexing of barcoded libraries resulted in ~ 20% data loss as unclassified reads and 1.5% read leakage. Conclusion The output of LIG was best (low noise, high read numbers of long lengths), intermediate in TAG (some noise, moderate read numbers of long lengths) and less desirable in PCR (high noise, high read numbers of short lengths). Overall, users should not accept assembly results at face value without careful replicon verification, including the detection of plasmids assembled from leaked reads. 
PY 2023
PD OCT
SO Bmc Genomics
SN 1471-2164
PU Springer Science and Business Media LLC
VL 24
IS 1
UT 001100595900001
DI 10.1186/s12864-023-09729-z
ID 96917
ER

EF