WGS sequencing of Synechocystis sp. PCC 6714 MT_a24
Illumina Nextera XT libraries- Sequencing on Illumina NextSeq, v2, 2x75 bpBioinformatic analysis:- Demultiplexing and trimming of Illumina adaptor residuals- Mapping of reads to references for Synechocystis sp. PCC 6714 (accession number CP007542.1) using bowtie2 (v2.2.9)- Variant calling using LoFreq (v2.1.0)- Coverage analysis with bedtools (v2.25.0)- Annotation of single nucleotide variations and small insertions and deletions with in-house software (four different views on the data: 1) all variations of all samples, 2) variationsProject: N269, Pflgl, Bacterial resequencing Page 2 of 2common to all samples, 3) variations not common to all samples and 4) variations exclusive to one sample)- Background filtering against wild type sample (PCC6714-WT)- Large InDel detection using Pindel (v0.2.5b8)- Assembly of unmapped reads did not yield any contigs