To assemble a wētā mitochondrial genome from raw Illumina short-read paired end data.
- Perform quality assessment of raw short-read data with FastQC.
- Use 01_run_array_subsamp.sl to take a random subsample of the raw data, as the complete data set is very large, and unnecessary to use in its entirety.
- Use 02_run_trimmomatic.sl to perform quality trimming and adapter removal of the subsampled data.
- Pass the processed data to NOVOPlasty for mitogenome assembly with 03c_run_novoplasty.sl. I originally performed this assembly in two batches, using a different reference seed for each. Here I just show the scripts used for a subsequent assembly using the assembled mitogenome as the reference seed.
- Map the processed subsample to the assembled mitogenome to check for errors with 04b_run_fastq_pipeline_loop_mtmodern.sl, a SLURM wrapper for 04a_fastq_pipeline_loop_modern_WGS.2.5.sh. This requires 05_make_coverage_plots2.0.R. This part of the pipeline is based on that produced by Sophie Cameron-Christie and Edana Lord for use in the Matisoo-Smith lab at the University of Otago.
- Continue assessment of quality and completeness with the online tools MITOS2 and tRNAscan-SE.