Draft Genome Sequence of prodigiosin producing Marine sediment-Derived red pigmented actinomycetes, Streptomyces sp. strain BSE6.1
The paired-end data of S2.1 was quality checked using FASTQC v0.11.8. Low quality reads and adaptor sequences were filtered using BBDuk. These filtered high-quality reads were assembled into contigs using SPAdes v3.12.0, IDBA and Velvet genome assemblers in a de novo fashion. SSPACE v2.0 was used to join the contigs into scaffolds with an iteration of raw read alignment over the three contig sets separately, to minimize the gaps. The 16S rRNA genes were extracted from the SPAdes assembly using Barrnap and was aligned against the non-redundant nucleotide database at NCBI. The complete genome of the nearest neighbour (Streptomyces sp. KPB2  Acc ID: CP034353.1) was used as reference to map the raw reads using BWA. After mapping to the reference genome, a consensus was created using samtools. The contig sets from the de novo assemblers and the consensus obtained from reference mapping were merged into scaffolds using CISA. Later, the scaffolds were sorted with the help of reference genome using MeDuSa. A final gap-filling step was performed using GapFiller and GapCloser to generate a draft genome. The draft genome was uploaded to RAST for annotation. A local annotation was performed using Prokka v1.12. The distribution of various coding sequences (CDS) was plotted using Circos.