Duplex Sequencing of bacteriophage lambda

Duplex Sequencing data of bacteriophage lambda. The bacteriophage lambda was grown by infecting MG1655 E. coli (WT) or MMR- E. coli (mutS). 4 replicates were done per condition. 1 sample contains pUC19 plasmid, grown on WT as a negative control. Samples were prepared as in Risso-Ballester et al. 2016 PLOS Pathog, and analysed using the duplex sequencing pipeline v2.1.4 (Kennedy et al. 2014 Nat Protoc) implemented in MIGALE. Briefly, after endpoint dilutions (to reduce phage diversity), mutations were accumulated in a single confluent lysis and the phages were extracted. Libraries were prepared at the University of Valencia with Duplex Sequencing adapters, containing a semi-randomized tag. After duplication of the two strands of each DNA fragment by PCR, the reads were sequenced. In the analysis pipeline, reads are clustered into families based on their tag identity. Then consensus sequences are built using 70% base identity of reads of a same family at each position. A second consensus is built using the base complementarity of two single strand consensus and mapped onto the reference genome. Mutations are detected by variant calling. The mutation rate of lambda was determined to be 100 to 1000-fold higher than its host. However, the studies that support this rate has a small reliability due to a lack of protocol and raw data. The aim of this study was to determine the mutation rate of lambda in a WT strain and compare it with the rate in a MMR (mismatch repair) deffective host, as MMR seems inactive during lambda infection, using Duplex Sequencing among other methods to determine the mutation rate. The mutation spectrum was also determined, to verify the presence of a signature for MMR inactivation during infection by lambda. The data presented here are raw reads for each samples and a metadata file containing informations for each sample. The pipeline used for analysis was used with default settings except a family size of 2 (default 3) as in Risso-Ballester et al. 2016 PLOS Pathog