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bsponge_chloroplast
README.md

README.md

bsponge_chloroplast

Supplement scripts and data files for the manuscript entitled "The signs of adaptive mutations identified in the chloroplast genome of the algae endosymbiont of Baikal sponge."

Description

The scripts on python intended to generage figures in the manuscript use several data files, provided with the scripts

python version 2.7 was used.

The data files consists of:

  • Choloroplast genome fragment, discussed in the manuscript, as a sequence file
  • Sequencing reads from five samples used in the study, aligned to the sequence of the genome fragment, in .bam format
  • Complete chloroplast genomes of several algae species in genbank format
  • Phylogenetic trees in newick format

The python libraries required to run the scripts:

  • biopython (1.66)
  • pysam (0.14.1)
  • matplotlib (2.2.2)

For the pie chart with counts of polymorphic sites for each gene (fig. 3 in the manuscript), the log file is provided with numeric values of the distributions presented in the chart (polymorph_distr.out)

mafft, fastme and readseq software is required to re-calculate phylogenetic trees

The software was used on Ubuntu Linux x86_64 server.

In addition, the scripts which could be used to assemble genome fragment from raw sequencing reads and a sequence of reference genome are provided. BioProject ID for the libraries of raw sequencing reads is PRJNA480194.