VIIGF

Alan E. Yocca aeyap42@gmail.com @Aeyocca (twitter) Uploaded 03-27-19

This is a horrible acronym but it keeps the file names nice and concise

Built for use on University's cluster. Compatible with SLURM submission system

• PBJelly part is still untested, working on that

Inputs:

• Illumina paired-end reads

• Reference genome

• Run just the viigf_var_inc step to get a consensus genome from incorporating SNPs into the reference genome

• I found marginal improvement after 3 rounds

  • test your own though, compare number of variants that still exist after 3 rounds

Configuration file:

• set variables to what you need them to be
• example configuration file: viigf_config_ragoo.conf

To set it all off!

• make sure the configuration file is set how you would like it to be set
• make sure reads are in either 01_raw_reads/ within ${WKDIR} or 04_trimmed
  • depending if they are trimmed reads or not
• run ./viigf_launch.sh
  • type: $ ./viigf_launch.sh without any arguments to see the command line options

viigf_pbj.sbatch

• untested as of 03-27-19
• additionally, code written to run MaSuRCA, prefer other assembly methods though
  • since my MaSuRCA build is fragile