IMPORTANT: REQUIRES COMPLETED TORMES RUN OUTPUT FOLDER WITH ASSEMBLED FASTQ FILES TO WORK
Short Script to Generate read depth of contigs from assembled microbial genomes in tormes output folders
Run after samscript - requires standalone datapane conda environment
activate tormes environment:
conda activate tormes
install samtools and bwa:
conda install -c bioconda bwa samtools
- Place samscript.sh in miniconda3/tormes/bin
- After activating the tormes conda environment enter: samscript <tormes output folder path> <cpus to use>
(leave trailing '/' off folder name)
Example:
samscript.sh /home/blogsj/tormesresults 24
Can be run from any location after running samscript to generate visualisations of contig quality data
needs a separate environment at this stage due to incompatibility with current tormes dependencies
conda create -n datapane -c conda-forge datapane=0.14.0 plotly
conda activate datapane
run meanlengthanddepth.py with an argument of the tormes results output directory after running the tormes pipeline and after running samscript.
Example:
meanlengthanddepth.py /home/blogsj/tormesresults
(again leave off the trailing '/' from the foldername)
Samscript will generate bam files for all sequences with fastqfiles in tormesoutputfolder/bams
Output from samscript will create files in tormesoutputfolder/genome_stats/<sequence>/coverage.report
eg:
#rname startpos endpos numreads covbases coverage meandepth meanbaseq meanmapq
NODE_1_length_98032_cov_38.894921 1 98032 52495 98032 100 80.1366 33.7 60
NODE_2_length_85910_cov_43.216245 1 85910 50938 85910 100 88.9155 33.7 60
NODE_3_length_80887_cov_39.732867 1 80887 44227 80887 100 81.8892 33.7 59.9
NODE_4_length_78948_cov_41.095878 1 78948 44560 78948 100 84.5851 33.7 60
NODE_5_length_78847_cov_41.004012 1 78847 44415 78847 100 84.3845 33.7 60
... etc
samscript will also generate files used by meanlengthanddepth.py to create visualisations of contig number, read depth and quality + DataTable of results for each genome. This data used by meanlengthanddepth.py will be in tormesoutput/report_files folder
Output from meanlengthdepth.py - will be in the tormesoutput/report_files folder:
