## Automation with Bash and/or Perl scripts could save you a lot of time... 10 pts. Read processing i. Investigate the read quality of the Illumina and Oxford Nanopore datasets. ## The error below can show up with FASTQ files containing long reads: ## Exception in thread "Thread-3" java.lang. OutOfMemoryError: Java heap space ## If so, use more threads with -t, e.g. -t 4 ii. Plot the read length distribution / calculate the metrics of the nanopore dataset. ## You can use Dr. Pombert's python script to do so: ## https://github.com/PombertLab/Misc/blob/main/read_len_plot.py ## Read lengths are very important for 3rd generation platforms. Because read sizes ## influence the assemblies, we should always verify their overall lengths iii. If required (and possible), filter accordingly. ## When using nanofilt, you can safely ignore the warning about pandas